I'm no expert on parts compatibility, but here's a partial list of what you might run into:

Tranny crossmember problems
Drive shaft lengths - front & rear
Tranny/TC bolt up problems - not sure if they're compatible.

The good news is that neither tranny is computer controlled, so you won't have to dig too deeply into the electronics side.

Also keep in mind that your gas mileage will drop noticably because the C6 has no overdrive. However, the C6 is a much more reliable transmission than the AOD.