Super T10 Issue? Drop it or not....?

HI guys, just put my 1980 Z28 on the road a month ago, which has a newly rebuilt Borgs Warner Super T10 4 speed in it and a 383 stroker.
The whole front subframe was switched out over the winter with a freshened up one with all new components and solid welded motor mounts. The car ran and drove and shifted fine, except sometimes it was hard to shift out of reverse because of the condition of the shifter and linkage. However, it was ok until I took it to get an alignment at Sullivan Tire and when I picked it up they told me that they broke 2 wheel studs off (brand new studs off of brand new hubs and brake parts..) and that because the studs broke off my rim was now warped and junk.
Ok, so after a little bitching about them test driving the shit out of my beater I took the car, and it was stuck in reverse in their parking lot.
I shouldve went back inside, but I was pretty eager to get the hell out of there so I went underneath the car and hit the reverse lever back out position so the car would be in neutral, and drove it home.
I go to back out of my driveway the next morning, and as I am backing up the car jerks to a stop suddenly as if it were an automatic tranny and I had thrown it into park doing 10mph...
Now when I start the car, with the clutch in so that its in neutral, and with the shifter in neutral (or in any gear), everything is peachy. But once I go to release the clutch (in neutral or in any gear), the car starts to make a rapping sound almost like a valve tap.
I have no idea what this is, and the only thing anyone has told me was that it could be the flywheel or the shifter? I put in a new shifter and even tried starting the car without a shifter in it and with all the levers disengaged and it still made the noise.
I'm scared to drive it around like this and ruin a newly rebuilt tranny that cost me a G...but I'm sick of getting rides to and from work and such..
DOES ANYONE HAVE ANY SUGGESTIONS? Any help would be greatly appreciated, I love this car but its been one problem after another so far and I've pretty much replaced or fixed every mechanical part on the thing at one point or another...
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