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Rhythmic knocking sound when clutch is engaged (pedal not depressed)

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Old 11-05-23, 08:39 PM
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Rhythmic knocking sound when clutch is engaged (pedal not depressed)

I've had a noise develop recently in my FB that seems to be coming from the transmission or bellhousing area. It's a fast knocking type sound, and it goes away as soon as I push the clutch pedal. I've also noticed that the car occasionally doesn't want to shift when it used to be butter smooth before. I've had random issues engaging first or second randomly, like the clutch didn't disengage. My first thought was throwout bearing, but it was replaced 1800 miles ago. I'd like to gather some opinions before I pull the transmission. Transmission front cover plate maybe (N204-16-220A)? Or something else internal?

More info:
S5 NA engine + FC subframe swapped in 1800 miles ago
Transmission is an original GSL-SE transmission, unknown miles
Clutch and pressure plate have 10k miles, resurfaced flywheel too
Throwout bearing and pilot bearing replaced with the engine swap, 1800 miles ago, along with new transmission fluid

Video (clutch engaged then disengaged):


Old 11-05-23, 11:40 PM
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pilot bearing?
Old 11-06-23, 08:41 AM
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The pilot bearing is pressed into the eccentric shaft to support the outboard end of the transmission input shaft. To me, it would be rotating as long as the engine is running, regardless of if the clutch pedal is depressed or not. Letting the clutch out is what engages the clutch disk and transmission internals to start turning. Could the clutch disk be rubbing against something? Was the clutch replaced 1800 miles ago too, with the throw out bearing?

Last edited by Banzai; 11-06-23 at 08:43 AM.
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Old 11-06-23, 09:10 AM
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I also didn't think it would be the pilot bearing. If it were bad, I expected it would be putting some force on the input shaft when the clutch is disengaged also since the E-shaft is always spinning.

The clutch and pressure plate (exedy stage 1) were replaced in 2016, about 10k miles ago. They sat on a shelf for a few years while I restored the car and built a new engine but I felt they had enough life left to keep using.

Throwout bearing and pilot bearing are brand new 1,800 miles ago, about 2 years ago. Pilot bearing is OEM and throwout bearing is Timken.

Last edited by derSchwamm; 11-06-23 at 09:20 AM.
Old 11-06-23, 11:31 AM
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maybe try draining the transmission oil and see if you find any clues there?
Old 11-07-23, 06:55 PM
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If it goes away as soon as you put pressure on the clutch pedal, meaning the clutch is still engaged, it is a throwout bearing or possibly a bent fork. New does not mean good.

If the noise only stops when the transmission stops turning, meaning clutch fully depressed and it takes a moment to stop, it is a bearing or a gear inside the transmission.

It physically cannot be the pilot bearing, when the clutch is engaged, it has no relstive motion to anything. The input shaft and eccentric shaft are turning the same speed.

There is a really slim chance that the eccentric shaft is loose, or a lightweight flywheel is loose on the counterweight, but that is not terribly likely.

Last edited by peejay; 11-07-23 at 06:57 PM.
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Old 11-07-23, 09:19 PM
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Thanks this confirms what I was thinking. I don't have a lightweight flywheel and the noise stops immediately with the clutch pedal depressed. I'll go ahead and pull the transmission out this week and take a look
Old 12-10-23, 10:11 PM
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I finally got the transmission out. Pressure plate shows a lot of wear at the end of the forks... more than a used and older plate I have on the shelf. The throwout bearing has some play on the shaft too, and might be a little loose in the fork? Not sure where to go from here yet. Pilot bearing looks OK though




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Old 12-12-23, 10:38 PM
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That is excessive wear on the clutch cover tines which are actuated by the Throw-Out Bearing. Theres either a misalignment of the critical distance provided by your flywheel and clutch cover dimensions or your Throw-Out Bearing is out of spec and being forced into the clutch cover with too much pressure. This would also destroy the TOB.

This clutch cover is an Exedy Stage1 with about 50k miles on it, with a Street/Strip clutch disk and Mazda OEM TOB. As you can see there's very little wear on the clutch cover tines, and this clutch behaved well until replaced with same, but new parts when I put in the aluminum flywheel. Have a look and compare with your posted pic;

You should only be seeing light contact marks from the TOB mating surface to the clutch cover tines.

My guess would be you have a bad TOB from the start (*wrong dimensions), as this is a much more likely cause than getting the clutch disk or cover installed incorrectly. Also, take a close look at your Clutch Actuating Fork for any deformation - this could also add pressure to the TOB. Hope this helps for comparison purposes,
Old 12-12-23, 10:57 PM
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Thank you!

With the wear my pressure plate has, should I go ahead and replace it? Unfortunately it only has about 10k miles on it but I'll do what's needed to get it working again, especially since the whole stage 1 Exedy kit is just $195. The throwout bearing was replaced without replacing the other clutch components less than 2k miles ago, with a Timken 614067: https://www.rockauto.com/en/moreinfo...&pt=1968&jsn=3

I can just get an OEM bearing next time to avoid any issues, though typically Timken bearings have been high quality in my experience.
Old 12-13-23, 04:59 PM
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I would replace the clutch cover (aka pressure plate), as the TOB surface which rotates with it must also slide along those tines, if you think about the geometry at play. With the one in your picture, you're likely to feel the TOB getting caught up on the wear spots as a rough feeling clutch motion. As previously mentioned, you really need to take a look at the parts you're putting in to figure out the cause - or you may be doing this again in the near future.

On the TOB you removed, how does it rotate? Is it frozen or "scritchy" when you try to rotate the section that moves on the clutch cover tines? Is it deformed or in some way damaged that would increase pressure against the clutch cover tines? Lastly, did you inspect your TOB fork, the ball it pivots on, and the assembled parts to make sure they love smoothly and freely? Best to get that sorted out before you put it all back together and in the car.
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Old 12-31-23, 09:20 PM
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I finally got a new clutch kit delivered and can compare throwout bearings. Interestingly the older Timken bearing does look a little taller. Laying them both down flat next to each other, I can see that the hooks for the clutch fork stand up higher and the cylinder itself is a bit longer too. It's not a huge difference but I'm guessing it doesn't take much. Other things I notice are a lot of wear on the bearing where it meets the pressure plate, and an overall good condition bearing (spins smoothly and doesn't sound bad). Still not seeing signs of issues with the fork or anything else.

Based on the difference in height, I assume I can swap the full exedy stage 1 kit in and have no issues moving forwards. I'll do the whole kit since the pressure plate and throwout bearing both needed replacement anyway.

Let me know if anyone thinks differently!








Old 01-01-24, 10:24 AM
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I think you nailed it. You can see that even the face of the TOB where it meets the clutch cover tines is flat on the old TOB and rounded on the new one. I'm of the belief hat the old one you installed was incorrect for the parts in hand and wore everything where it shouldn't. He new one looks correct, and as you stated, there isn't any other deformation or damage to parts which would account for the wear pattern you saw.

Installing all new parts will fix this for good. Nice diagnostic work on it, and let us know when you get it back together,
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Old 01-01-24, 01:43 PM
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I was getting started installing new parts and immediately noticed issues with my flywheel. And I suspect a leaky rear main seal...

I assume these cracks are not worth machining out? It was already machined once before I installed it. I also assume a GSL-SE flywheel (that I have on my shelf here) won't work with an S5 engine? They have a noticeable weight difference. I'm going to be safe and go ahead and track down another one



Old 01-01-24, 02:40 PM
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You're out of material on that flywheel. Not knowing how much was lathed off in the prior operation, it's now showing voids within the metal that will grind up a pressure plate quickly. As to fitment on your S5 engine, the S3 series have flywheel matched to the front counterweight. You could likely find an S5 flywheel and use that with no concern about mismatched weights, but you need to be sure what's on the front of that engine. Another approach - the one I chose - was to go lightweight aluminum and use the matched counterweight from the automatic, making this flywheel the last I'll ever need (*it has replaceable friction material), and being an SE has the 225mm diameter of the later generations for ongoing clutch disk and pressure plate replacement.

You're going about this the right way to ensure you only have to do the job once. Finding the right parts is just an investment in your future satisfaction and enjoyment,
Old 01-02-24, 10:19 AM
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Thanks, after doing some research and so far failing to find an S5 NA flywheel for sale I ordered the racing beat lightweight steel flywheel and s5 counterweight. Another $600 on top of $200 for the clutch kit. This little repair got very expensive but I am excited for the flywheel!
Old 01-03-24, 10:00 AM
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Well, since you're replacing the flywheel, the rear main seal will be right there and accessible if you think it's leaking (*that's rare). Once you have the flywheel safely off, you'll see how easy it will be to bolt up the automatic counterweight and hen install your lightweight flywheel to it. Very straightforward and easy with a torque wrench and some patience.

Unless you live in hilly country (Germany), the lightweight steel flywheel should be perfect for spirited driving. I went lightweight aluminum because I live in the Sonoran Desert and it's very flat here for 90% of my driving. In spite of that, I have never been able to smooth out my idle to where it was with the stock flywheel; that extra mass of the stock part made for a nice, consistent idle. Going lighter means there's less tolerance for ignition misses, intake pulses, and other variables that contribute to minormvariations in combustion - as you've removed the shock absorber for the system (*rotating mass). The RB aluminum flywheel is only 13lbs, plus the counterweight. I've just gotten used to it, and accept the tradeoff for better revving performance.

At least now you'll have 100% confidence in your Clutch when you get it all back together. That TOB you're replacing was the culprit. The surfaces and dimensions are all wrong...
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Old 01-05-24, 09:46 AM
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In my forum research I learned a lot about lightweight flywheel tradeoffs but I didn't see anyone who regretted installing one. People seem to love them, and I'm sure I will too. I do live in a hilly area but I'll survive (central Texas).

Regarding the rear main seal, it's definitely leaking. It was a new Atkins seal 2 years ago and this forum actually has a lot of people complaining about the Atkins seals not sealing well. Apparently they use thinner RX8 seals and sell them in their rebuild kits. I ordered an actual RX7 OEM part and it should be an easy swap right now. I won't buy another from Atkins though

Old 01-28-24, 06:03 PM
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I wish I had a better update but the noise persists. It took me a while to finish the FB since my daily driver also had some issues to deal with, but from the first start up with the new flywheel and clutch kit the noise was there. I'd post another video but it's the same as the original one.

I'm a little stumped now. The only thing I can think of it the transmission input shaft bearing? The shaft itself had a small amount of play and didn't feel 100% stiff like I expected but I don't have a good frame of reference. Any other ideas?

I did go buy the harbor freight transmission jack today since it was on sale. I am done pulling the transmission without one...
Old 01-29-24, 07:02 PM
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When you push the clutch pedal down, the noise gradually stops? This could be a transmission bearing, but at least with the trans dropped, you can take another look at the clutch cover and Throw-Out Bearing to be sure they're not dinged up like the last one. The front cover of the transmission includes the pipe section(*nose) where the Throw-Out Bearing rides, along with the pivot ball for the clutch fork to ride on. Once removed, it exposes the big bearing which carries the load from the input shaft to the transmission. If that bearing is bad, you can replace it fairly easily, but if that bearing is bad, the rest of the main bearings in the trans are just as old, so a rebuild may be in order.

Also, you're not referring to the input shaft bearing and grease seal in the end of the eccentric shaft, are you? Did you change that with the new clutch, or leave the existing one in place? In my experience, those can grenade impressively and lead to all kinds of noises from the trans, but usually goes quiet when the clutch pedal is out, and trans is in neutral, as the trans input and engine are bound together at that point with zero slip between them. Pushing in the clutch decouples them, and requires the input bearing in the eccentric shaft to keep things centered as it spins. When these run out of grease, or get corroded, they can implode and you'll know riht away when you stick your finger in the eccentric shaft end - it'll come out grey with metal dust.
Old 01-29-24, 09:36 PM
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When I push the clutch in, the noise stops basically immediately. Which is frustrating because I understand the logic of the transmission spinning down slower. I might drive a bit more and see if it spins down noticeably when I go from a gear into neutral.

I was previously planning to replace the transmission front cover and gasket but since it looked fine my throwout bearing looked wrong I skipped it. I still feel like there might be too much play in my transmission input shaft though (see video in post #8).

I did not replace the pilot bearing because it looked and felt fine and has less than 2k miles on it (it's an OEM bearing I installed when I built the engine). No metal dust in it that I noticed. I have bad memories of spending 5 hours trying to remove one from my FD, ultimately ending with a dremel so I prefer only to remove those bearings when they're old or bad. And like you said, I would expect to hear that noise when the clutch pedal is depressed, not the opposite like I am hearing.

At this point I feel like I just need to track down a new transmission or look into rebuilding mine, but I'm honestly not sure


Old 01-30-24, 09:50 AM
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Symptoms don't match with Pilot Bearing failure, but you'll be able to visualize it wih the transmission removed. Stick your pinky in there and be sure it has a dab of grease on the seal, and you should be fine.

The transmission on our cars is pretty solid design and can be rebuilt by a gear shop if they have access to the riht bearings. Apart from that, the 2nd and 3rd gear synchro rings should be replaced while it's apart (there aren't any on 1st, 4th or 5th) and they're still available from Mazda, as they were used in many cars of the era. Check MazdaTrix for those. You CAN rebuild it yourself, as there's not any critical adjustment for gear mesh, or crush washers or anything like that. Once you see one apart, it's dead nuts simple.

Depending on where you live and what speed shops are around (*that you trust), I'd take the trans around and let them quote you on rebuild pricing. I would definitely go with a shop that's familiar with Mazda and has access to the right metric bearings. Let us know what you find,
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Old 01-30-24, 09:50 AM
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Drove to work today. I think I hear the noise at low speeds, like 1st/2nd gear driving in a parking lot. I also think it doesn't stop as immediately as I thought but gets quieter quickly, so maybe I am wrong about how immediate it is. I'm going to keep driving and see, but if I can 100% confirm I hear the noise while in gear too then I assume the transmission just needs a rebuild (or replacement). It doesn't help that the whole car is noisy though, including a whining rear diff!
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