Transmission Problem

I have a '94 EX D16z6 and swapped out the auto for a manual about, S20 maybe out of an SI, 40K miles ago. My throw out bearing has been making some niose so this weekend I pulled out the tranny and put in a new clutch, pressure plate, throw out bearing and pilot bearing. Today while driving something popped pretty loud while getting ready to take off from a stop sign. I have only put about 200 miles on the new clutch kit and I have not taken off hard, shifted hard or anything even remotely abusive. Even when it popped I had barely even let out on the clutch. The tranny is not really making any noise while the engine is running. I can move through all of the gears with the clutch in or out and nothing happens. I have pulled the tranny out of the car yet, but hopefully you can shed some light on this situation before I pull everything apart.

Hate to be obvious, but it could be ALOT of things, worst case, the the input shaft snapped and the trans is junk (but that should case shifting problems, and VERY unlikely, but hey you asked). Most likely, one of the parts you put in is defective and gave up. There is no pressure holding the disc to the flywheel is the engine rpm doesnt even drop when the car is in gear and the pedal is out. Another possibility is that the part that broke could damage the flywheel, which would suck.

Okay I took the tranny back out tonight and I found that the passenger side drive axle had popped out. I am not really sure why this popped out, but I thought that I had is seated good. Maybe I was just in a hurry and missed this.:banghead: The clutch and everything else looks good. No problems with the input shaft. When I turn the input shaft both gears for the drive axles spin. I can go through all of the gears and no noise. Would the drive axle being out cause the car cause the car to act like it was not in gear? I would not think that it would cause this problem, but I am not really good with transmissions.