1992 Saturn SL2 Transmission grinds sometimes

Okay so recently the clutch went out and it was parked for about a month until I couls replace it. Qhen I finally got to replacing it there was a hole the size of about two quarters in the bell housing of the transmission around where the shift fork and throw out bearing sits. So I went and pulled the bell housing from another car and got it all back together. I replaced the clutch, and reinstalled the transmission, but now the it doent shift right. 1st and 2nd gear work perfectly fine, but when I shift into 3rd, 4th or 5th it grinds and doesnt go into gear. Reverse works fine. I recently replaced the master/ slave cylinder assembly also as it was damaged in removal of the transmission. Im thinking its gotta be in the linkage somewhere any suggestion? Anything?