knobs

ok i need help, so my original top shift t-case that i had in my 1987 4runner, the shifter went out, i had a spare top shift so i swapped them out, this was my first time swaping in a tcase, when i got the new one in, i had to draw the last 1/4" in with the mount bolts, and both outputs were competley locked up with the tranny in neutral, so i was going to take the shifter out of the one that i swapped in and put it in the original one that had the shifter sieze. so i went to remove the one that i swapped, it came out about 1/2" and then it wouldnt come out any more, the input shaft is completely stuck in the tranny, i have pryed, beat and done everything else and im so confused as to why it would be stuck in, i feel like a dumbass and i dont know what to do! please help!