92 4x4 Auto to NV5600 conversion question

[ihegdal]

My son wore out the auto in his 92 and decided to convert to a 6 speed. He started the project without doing any research (he's young). Today he attempted to mate up the transmission with the engine and found out that the crank shaft is not machined to accept the transmission input shaft.
I didn't see what he had first hand, but it sounds like there was no pilot bushing/bearing and no place to put one.

Is the crank for an auto different from the crank for a manual transmission.

Has anybody else encountered this?

Any recommendations?

Ian