If you’re referring to the stub on the torque converter nose this usually fits into a recess in the crankshaft. If it will not fit then there was likely a production change somewhere along the line and the engine is incorrect for the year and VIN range.
Theorizing here for a minute, did this new used engine come out of a Jeep with a manual transmission?
If so, it could be that what’s holding you up is the pilot bushing or bearing in the end of the crankshaft. A vehicle with an automatic transmission will not have this bushing.
If this is the case remove the pilot bushing/bearing and see if the converter stub will fit then.
As to the poster with the rebuild comment prices will be all over the map and in my opinion a shop should not even give an estimate on something like this except in a vague general sense. (About 5 grand…that kind of thing.)
Generally an engine that has been through what that one has gone through is really not worth rebuilding. The cost of parts and auto machine shop work alone makes it a lose/lose situation.
I’d go with a low miles salvage yard motor.