The service manual says 71-76ft-lb for the flywheel bolts and 14-19 for the pressure plate. The large bolts securing the transmission to the block have a torque spec of 65-86.
As far as I know, the bolts are re-usable. Though, when I installed my Fidanza flywheel, it came with new bolts for the pressure plate, since the threading on the new FW was different.
As to your other question, the pilot bearing gets pressed into the center of the FW. You can use a rubber mallet to gently tap it in there. The clutch kit I purchased recommended using a bit of loc-tite on the outside of the bearing.
Replacing the axle seals is not a must, but if they are more than a few years old, it's good practice to replace them as long as you have the axles out.
The service manual recommends applying a small amount of grease to the input shaft on the transmission, as well as at all points where the throwout bearing comes into contact with the transmission.
Finally, yes you must drain the transmission. If you don't, as soon as you pull an axle out, you'll have 2 quarts or so of transmission fluid on the garage floor before you even know what happened. I speak from personal experience. lol
I'm aware the OP has probably already replaced the clutch, but I'm seeking some info myself, so hopefully this gets me some good forum karma! haha
