Installing The Clutch And The Transmission
1. Install the flywheel. Use new bolts and tighten to 40 lb-ft + 180 degrees. Tighten the bolts in stages and using a star pattern. I tightened all 8 to 40 lb-ft followed by 90 degrees for all of them and finishing off with another 90 degrees for all 8. Mark the bolts so you don't accidentally over torque them. To prevent the flywheel from turning, find a suitable open ended wrench. Wedge it against one of the guide dowels and have a helper hold it in place as you tighten the flywheel. This method is strange, but it's free and it works. A better method is to buy the Audi 3242 Crankshaft Lock Tool and use that to keep the flywheel from moving.
2. Use the clutch alignment tool to align the clutch disc and then install the pressure plate. Use new pressure plate bolts and tighten to 18 lb-ft
3. Next step is to install the transmission. Just take it slow and make sure that the shift rods and slave cylinder do not get pinched by the transmission. You will want to have a second person helping you guide the transmission in.
4. Tighten the transmission bolts using the torque specs below.
5. Install the transmission mounts and tighten the bolts to the following specs.
6. Install the slave cylinder and tighten the bolt to 15 lb-ft. I had a lot of trouble with this step. You won't be able to slide the cylinder back in with your hand. Find a screw driver and bend it a little. Feed it into the mounting hole and use it as leverage to slide the cylinder back in. Slightly rotate the the cylinder back and forth as you feed it farther inside the transmission. Once it's all the way in you will see that there is a little indentation on the transmission where you can rest the cylinder without it popping out. Hold the slave cylinder in place with your hand while installing the bolt.
7. Connect all the electrical sensors. The engine speed sensor needs to be tightened to 7 lb-ft.
8. Install the drive axles and tighten all the bolts to 30 lb-ft.
9. Install the shift rods. Tighten the shift rod to 17 lb-ft and the pivot rod (the 8mm allen bolt) to 30 lb-ft. Yeah, good luck getting a torque wrench in there :).
10. Install the drive-shaft. Tighten the front and rear bolts to 41 lb-ft and the center support to 17 lb-ft.
11. Install heat shields over the drive axles. Tighten to 17 lb-ft.
12. Install exhaust. Tighten the exhaust pipe to manifold bolts to 18 lb-ft. The exhaust bracket bolts should also be torqued to 18 lb-ft.
13. Cross your fingers and start the engine.