Ok, I just changed the transmission in my car with a stock 90 LS y1 rebuilt tranny, and its running sweet 
Got a 90day warranty on the tranny, and everything on it is running super smooth - except for the shift form 2nd to 3rd at high RPM. I know this sounds like a synchro problem, but its not. For one, its a new transmission, and the 3rd gear synchro is fine. For two, I double clutched, and it still didnt shift smoothly. And for three, it was doing this before I changed my transmission.
Heres what happnes: when I get around 4k rpm, and shift up to 3rd gear, I can hear a small grind sound, and it is harder to push the shift know into place. The grind sound however doesnt sound like its comming form the tranny, but the area directly underneath the shift knob. Heres what i want to know… My shifter is extremely loose, and I think it needs new bearings. I am wondering if the grinding sound I hear could be something to do with the bearings rubbing against eachother? Im not too worried about it, its just annoying when other people are in the car, and it grinds when i shift about 4k rmp. Like I said, I dont think its the tranny; i think it has something to do with the shifter. Ahh well, im not too worried about it… Just wanted to know if that could be the problem, and to hear what you guys think it might be Thanks