Here are the latest pics.
In this one you can see the engine is centered with the tranny crossmember. If you notice we had to cut some material out of the arch in order to clear the tranny:
In this pic you can see the tranny is sitting on all three spacers, the shift tower is protruding way up into the hump, and it is rubbing on the right side of the opening in the hump:
Here's a close-up of that rubbing issue:
Here is a pic of the relationship between my oil pan and the center steering link. This is with all three spacers holding up the back end of the tranny:
As far as the 4-speed hump goes, I don't know how it could be wrong. It was an original hump that came out of an E-body. It can only go in one location, and when it went in it fit like a glove. I don't know how it could possibly be out of location side-to-side.