The only two things that come to mind are: Maybe the new hinges are aftermarket and don't have the same size pin to match the older hinges.
The hinges are not in line/have matching angles and they are getting into a bind when you try to lower the door down. To install a different set of doors on a Jeep, the door must be set to the body, the stricker post set up to match the door, the windshield slope then set to the doorframe, and if needed, then the hard top to fit......all using the "floating" nuts behind the adjustable hinges in the doors and lower mount.
Can you measure the shaft vs the hole and see if there is indeed a big difference as there should be no need for "prying".
1975 CJ-6 304 T15 Dana20 30/44 3.73
1983 CJ-8 258 T5 300 30/44 3.31 Looking for full or half hardtop buy or trade
1986 CJ-7 Laredo 4.6 stroker T5 300 30/44 3.31
1986 TJ-7 Trail Jeep project in the works
2003 Inca Gold TJ Rubicon