If you used one of those plastic input shaft tools, that is more than likely the issue... I used one last year and I about lost my mind trying to slide the 18-spline trans back in with a fresh Mcleod clutch! I ended up borrowing a friend's NOS input shaft and it worked like a charm

'70 Super Bee 440 6 pack 4-spd 4.10 Dana N96 EB5
‘70 Super Bee 440 6 pack 4-spd 3.54 Dana FC7
‘70 ‘Cuda 440+6bbl 4-spd 3.54 Dana N96 EB5 V1W