1995 honda fourtrax 300 output gear wont go all the way back in

hey guys i am new to this forum but i have a project 300 going on right now it started off as a 2wd and im doing a 4wd conversion i had a running 2wd and a parts 4wd with a bad engine so i took the motors apart and combined them i took all the left covers and left side of the crank case off the 4wd and put them on the 2wd engine and everything went smoothly until i got to the output shaft it will go almost all the way in other than about 1/2" of it i need help figuring out why it wont go in