BoostedSS

I had a problem with my clutch sticking to the floor so i replaced everything in the clutch assembly except master cylinder. After 400 miles of light driving i punch it in second gear and hear a noise. After that i would get a grind when i would up shift during normal driving, and would grind so bad at full throttle and high rpm, i couldn't upshift. You can't hear it but can feel it in the shifter under light throttle , normal driving. I replaced my dirty clutch fluid, after a while of driving it seemed to go away. I was able to beat on it with no problem( never shifted the car without getting off the throttle). After a while i started getting very bad chatter and grinding noises comming from the clutch/flywheel area, and if i let go of the clutch to hard with throttle i get a loud grinding from the same place. Then i start getting terrible vibration over 4 k rpm. It vibrated the whole car pretty bad, like an fbody would with the pinion angle set wrong on the torque arm. I take it in to a shop to get the clutch replaced, and the find that the pilot bearing was completely chewed up, which cut into the input shaft, bent my driveshaft, and messed up the torque tube. I replaced everything, including clutch. After a few hundred miles the grinding when i upshift comes back, and it vibrates at full throttle, only this time i can pinpoint it comming only from the back where the trans is. My clutch is fine and doesn't slip at all, and i get no noises from the clutch. Two days ago, the grinding and vibration go away! Even at full throttle(didn't try full throttle shifts just in case).
Im planing on getting the trans rebuilt, but would like to know what the hell is going on here to avoid any surprises when the trans gets torn apart. What is causing the vibration and grinding? They both seem to present in the same time, and both go away together. Can this be syncros and forks or something worse?