After doing a few searches on here, I was unable to find an exact answer to some of my questions.
First, when applying grease to a needle pilot bearing (89 gtus) can I use wheel bearing grease, and should I apply it to both the inner and outer race?
Also, which direction does the seal go in? Should I place the pilot bearing in just deep enough to allow the bearing seal to sit flush with the flywheel nut?

And as for my input shaft, it has a bit of rust on it. What is the recommended procedure for removing the rust? I was going to use 320 grit sandpaper, then finish it with 800 or 1000 grit.

Thanks in advance for any suggestions!

 

it just acts as a guide to keep the eshaft and trans shaft straight.
The pilot bearing can be put in and the Seal can sit flush to the shafts recessed lip.but not to far that you'll have a hell of a time getting it back out IF you have to do so again.
Input shaft: clean it up,rub a touch of grease on,BUT not excessively as the spline is mated to the clutch plate and you do not need grease coming in contact with that surface area.

Tip: a 10/11mm deep socket is a handy tool to install the pilot bearing..tap lightly..don't kill the edge and you are fine,.

 

If you don't have a special tool to install the pilot bearing, another option is to use a body hammer to do it. It has a wide flat head and it's light and controllable. Just be sure to start the bearing evenly and strike the bearing evenly with quick, light taps. Once started, increase how hard you hit it until it starts going in. Patience, it's not a nail. Then counter-sink it with the old pilot bearing or a socket as Styx said. Careful not to get too much grease on the bearing or the hydraulic pressure will prevent the input shaft from inserting all the way and the trans. won't mate up. I don't recall there being a "front" and "back" to the bearing on the ones for my car. I assume the same for the FC.

 

Thanks for the advice everyone, I ended up getting it installed using a heavy hammer and a 14mm deepwell socket, I had to sand down the OD of the socket to allow it to press the pilot bearing to the proper depth.
Another question:
I installed a new throwout bearing today, and was testing it before I throw the transmission back into the car, and noticed that the bearing gets caught up on the shaft when I extend the shift fork all the way. Is this normal? I compared the new bearing to my old one, and noticed that the new one has a slightly larger lip/land on the inner race than the old one, is this due to wear, or is it a wrong bearing?

 

Depends. Is the area the bearing gets caught beyond the normal travel?

 

This

If the TB isn't pressing against the PP it may travel farthur on the input shaft than it should