I decided that since the transmission is out that I would go ahead and replace the input shaft seal on the transmission. The seal itself is pressed into what's called a sleeve guide. The sleeve guide has an o-ring and is bolted to the transmission. When I went to the dealer to get all the parts they told me that they do not sell the o-ring separately and that I would have to buy the whole sleeve guide. The new sleeve guide comes with the o-ring and the seal already pressed in. The cost was $95. If you do not want to replace the o-ring then you can buy the seal and follow the steps bellow on how to change it out.
1. Follow the steps in Audi A4 Clutch Replacement Guide to remove the transmission.
2. With the transmission removed, unclip the release fork and remove the fork and release bearing as one unit.
3. Continue by removing the torx bolts that are holding the guide sleeve.
4. Slide the guide sleeve out. The seal is actually pressed into the sleeve. Notice the o-ring - replace if damaged or worn out.
This is the tool I used to remove the old seal.
Or you can buy a new guide sleeve with new o-ring and seal pressed in.
5. If you chose to replace just the seal, press it into the guide sleeve. Slide the guide sleeve back in, careful not to nick the seal against the input shaft splines. Use new torx bolts and torque to 26 lb-ft.
6. Slide the release lever and release bearing on the guide sleeve, making sure that the retaining clip engages the lever on the bottom.
7. Reinstall the transmission by following the final steps of the Audi A4 Clutch Replacement Guide.