Sure you can use a manual engine in an auto car and vice-versa...

To use a manual engine in an auto, you need to swap the flywheel AND remove the pilot bearing from the manual engine...

To use an auto engine in a manual car you need to swap the flywheel AND install a pilot bearing in the rear of the crank...easy peasy..

I just bought two M54 B30's with problems for $100 total.....one was hydro-locked driving thru a car wash (likely has bent connecting rods) and the other was a race engine that lost its oil pump sprocket...

Hoping I can salvage at least one of them...I have spare M54 blocks, heads, cams, etc.