You have a few issues here:

1. You posted in an Archive.
2. There is an adapter plate between the engine and bell housing, and they are different thicknesses for the stick and auto transmissions. However, they are not 0.5" thick.
3. It does sound like you have a problem with the snout of the trans and that could be that you have not 'screwed' the internals of the torque convertor in properly. There is an installation sequence discussed in the FSM (factory service manual) that you can find at mitsubishilinks.com...remember to drop a small token if you download anything.

Russell