95: The clutch assembly isn't part of the transmission - it's attached to the flywheel. When you pull the tranny, the clutch assembly remains behind, on the engine. I retained my original assembly in the swap.
Brick, your comment and another page I just read suggests it may be the bearing supporting the input shaft hanging up a little:
http://www.drivetrain.com/clutcharticle.html
Quote:
There are two potential bearing-noise makers in the clutch system-the release bearing and the pilot bearing. To determine which one, if either, is making the noise follow these steps:
Step 1 With the engine running and the transmission in neutral, if the noise occurs it is in the transmission, most likely the front bearing supporting the input shaft.
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If that's it, it's not a huge deal. I can simply key-start the engine when I occasionally can't get the shifter to go in. I'm not going to pull it apart again any time soon
I would however still like it to be a linkage or cable problem.