98 fourtrax 300 really screwing with my head

alright to start out last winter i was riding in the snow u joint snapped and locked up, cracked output shaft housing. pulled motor and replaced that whole unit. i also have another fourtrax i was just rebuilding everything went great with that one. but i realized that i had put the gear that sits closest to the left hand side of the case in backwards. so i pulled it and flipped the gear put it all back togther and started it but the tranny was locked up. sounded as thought it was under load in nuetral so i pulled it and split the cases again. disassembled and reassembled the tranny, now it spins in nuetral, but as soon as it shifts into reverse it wont spin unless i take the reverse gear out. same with first gear. it will not spin in either of those gearswhen those gears are installed. and have a bunch of extra parts that a bought a while back, so i swapped all gears out and countershaft and main shaft shift forks and the rod that goes through them, the only thing i havent swapped on the tranny is the shift drum. any ideas?? anything is appreciated.