I had to change the transmission in my first car for a different year junkyard tranny. The length of the tranny was fine, but I had the same problem - the torque convertor didn’t fit onto the crank gear. I brought the tranny back and ultimately got one that did fit.
It MIGHT be possible to buy the correct torque convertor and replace your existing convertor in your existing transmission. I’m sure someone will jump all over this answer if that is not possible for whatever reason.
I doubt you want to remove the engine and start over at this point. In the end, maybe replacing the transmission to match the engine will be necessary. Of course, you may run into other issues - length of the transmission comes first to mind. This will in turn require a shorter or longer drive-shaft.