Thanks again for all the suggestions... a little bit of information from troubleshooting a couple days ago: the noise is not present when the wheels are not spinning i.e. the transmission is in neutral with the clutch in or out and when the clutch is pushed in and the wheels have stopped turning. This means that the noise is not in the clutch or the transmission! When the drive shaft was shortened the u-joint at the rear yoke came apart (one of the bearing caps fell off) and I repacked it. Wondering if this is the problem? A piece of floor dry or a missing or misaligned needle would be all it would take right? As you can probably tell I do not have a lot of experience with this stuff... but I am learning.