Jeep engine problem

I have a 1991 Jeep wrangler that I recently blew a rod through the engine block, I recently bought a 1991 engine for the jeep, but the engine is automatic. My jeep has a standard engine. I want to make the automatic engine work. the pilot bearing in the standard engine does not fit into the automatic engine because they were not made to be converted. I believe that it is possible. Anyone have any ideas?

ok, the engines will be the same. the transmission is the part that is either automatic or manual(standard).
what has been done so far? is the old engine out of the jeep? is the transmission still in the jeep?

in a nutshell, you want to swap ONLY the engine, that means that stuff like the flywheel and bell housing from the manual trans will need to be kept(they are different )