After resolving an issue of my back brakes locking up after they heat up (Adjusted the push rod at the master cylinder and then readjusted the brakes).  I recently started experiencing some "chatter" when taking off in first or backing up.  The clutch looked good when I had the engine out back in Feb.  After driving up Raccoon mtn pump storage and back and the brakes locking out in the rear recently I was wondering if this is more of a clutch issue or a Transaxle issue.

Scott is correct about the bowden or flex tube. It has to have about a 1inch deflexion or bow in the tube from the body to the tranny and no broken ends.
    Also bad tranny mounts can be broken and hard to see somtimes. The nose cone mount is nortorious for this. The cradle mounts (at the engine) can be separated causing the engine and tranny to move around. You can check these with a pry bar. Try to lift the tranny up with the bar.
    A warped pressure/disc or hot spots on the flywheel can cause a "chatter". Any signs of oil ?

Shucks !!! You got the whole cookie. The flex tube is the #1 culprit but you should know that you don't go to a gunfight with one bullet for your M-16 to solve a problem.