Lots of different noises from transmission. Need help with diag
 

Brace yourself because this is a long one:
So about a year ago I was struggling with a transmission scraping noise. Turns out it was the tail shaft busing that was completely shot but while I was taking the trans out I thought I would pay someone to rebuild it with new synchro's (3rd and 2nd were hard to shift at high RPM)
Well that rebuild was about 10 months ago and I barely drove it because of a radiator issue that popped up right after that (and I went a rebuilt the motor too). Now im driving it again and after a few days of normality its making all kinds of noises that dont sound good. I will list them below:
First real noise was right after I drove it a short ways to get something to eat. After I parked it in my garage I stuck it in neutral and after about a minute or so it started making a bearing whine. Fairly loud and definitely noticeable. Went away the second I engaged the clutch. Decided to turn off the engine and diagnose it at a later date. I HAVE YET TO HEAR THIS AGAIN!

Second noise was when I got the car on jack stands and let it run in neutral. I had the front end off the ground so the car was at an angle. This time, the transmission was making a completely different sound. You know the clattering sound when gears come together? That was the sound but it was on and off. it would make it for one second, then stop for two, rinse and repeat. The sound was coming from the back of the tranns (by 5th and reverse, that extension before the rear bearings) I stopped the car and checked fluid; thought it was a little low (at the time this was the original fluid that was in the tranny when it was rebuilt).

Put the car down and drove it. Clattering sound increased in volume with RPM. didn't get to the nearest intersection (~1/8th mile) and the whine sound came back, but this time it only occurred when in gear, unlike the previous sound where it would happen in neutral. It was also not as severe, but only slightly (was still bad) Additionally, the sound only started in 3rd, was the worst in 3rd gear and would increase in severity with vehicle speed. Drove it back into the garage.
Got the car on all 4 jack stands so the trans was level and checked fluid again and the level was fine. Decided to do a drain and fill on the trans.
Did the drain and fill and this is what the old trans fluid looked like: mostly black with glitter showing. not much metal on the plug magnet. Again, this was the fluid that was used when it was rebuild 10 months ago.
https://cimg9.ibsrv.net/gimg/www.rx7...adfd06f692.jpg

Finished filling with new fluid and ran the car in the air. gear clattering sound was present but was barely audible by ear (if you put your ear on the gear stick you would hear it). Still not happening all the time either when in neutral and clutch engaged. Additionally, the whine was significantly less prevalent, but I was not sure if that was because it was in the air or because of the new fluid.

Wanted to get peoples thoughts because this transmission is giving me all kinds of different signs and I can barely make heads or tails of it.

Update: mystery getting weirder, but I got it off the jack stands and was about to take it for a drive. put it in first and slowly let out the clutch. As I was creeping down my driveway, I heard a loud grinding noise followed by a shutter (the grind sounded like what it would sound like if you missed a gear, except I wasn't changing gears. it was abrupt and the durations was about as long). I immediately stopped and put the clutch in. after I turned the car off, looked under for any leaks or damage (thought I might have run over anything but there wasn't anything there) I turned the car back on and let the clutch out. no sound. Put it in first and crept forwards, still no sound. started making my way down my street and going through the gears (still keeping my speed low just in case). still nothing. Eventually I mustered the courage to go faster, and it drove like normal (maybe a light whine from 1st to 3rd, but nothing major).
Idk what the heck is going on but I don't trust this thing. I still have yet to go on the main road and I don't think I want to for now -_-

I'm not an expert on transmissions, just a dude who does its own repairs.

First question would be: Does the sound come from the transmission. Most of what your desrcibing could be differential noise.
If you put it on jackstands and it can be shifted indifferent gears without crazy noise, it's propably not the transmission.

well the sound only happens now when its in gear and clutch engaged. if you disengage the clutch and roll the car like I did to get it back it doesn't make any noise. I'm hesitating to say throw-out bearing but that might be what it is as the sound increases in volume and pitch with RPM speed not with vehicle speed.
Additionally I think there is a temperature factor in this as well. My last post said the noise went away but I only drove out arround the neighborhood for a few minutes. Just this morning I decided to take the next step and drive it (very cautiously) on the main road and after a few minutes of regular driving it started making that noise again.

When the shop put your trans back together, did they shim the front bearings correctly? If not, your input shaft can rub on your countershaft. Will be noisier at higher rpm and speeds.

Yes, they did. I actually watched them tear it down and they mentioned that about the shims.

Look at this video!!

Clutch in and out!!
I have EXACTLY the same whirring sound since i bought the car in 2015. Did a few gearbox fluid flush. It was'nt worse over time. It's the gearbox input shaft bearing! You should drive the car for many hundred thousand miles and it will not get worse. You can live with it forever.

Did you rebuild your transmission at all? that sounds similar but I think mine might be louder (hard to tell with the video). I think your right, the only thing that is concerning me is some of the near bearings I got were from RockAuto and some of them had metal guards on one side of the bearings while the originals didn't. The other thing is that it didnt start right away. I drove it about 150-200 miles before having issues like this.

No rebuild at all!

The only thing you can do for "gearbox safety" is to change the fluid and add an antifriction additive!

I tried Castrol Syntrax first and i wasn't happy!

Then i tried Valvoline gearbox fluid and it's much better. During fluid change with Valvoline i added an H-Bn (Hexagonal Boron Nitride) anti friction additive

This one
https://www.beps.it/it/additivo-olio...c_1213632.html

(i think it's discontinued through Amazon now.......it was 3 years ago). It's sold only in Italy just now

But........EVERY anti friction H-Bn additive for gearboxes is good........Barhdal, Liqui Moly....etc!

Now the noise i hear inside my car is a lot quieter than the noise of the video above!

However this is only an "hearing" problem! You should drive the car in saftety without the worry of serious gearbox damage!

You should worry if the gears became hard to insert!

Anyone have any experience with a company called "US Standard Gear"? that was the kit I bought from rockauto to do the transmission rebuild. was wondering if anyone else has done the same and what their experience was.