Okay, this is going to be a stupid question - While I'm waiting to get my engine rebuilt for my 73 super beetle it occurred to me that I might try and put the engine out of my 72 standard beetle into the super. Will this work? I mean do I have to have different tin, different heater boxes, muffler, etc.?

From the doors back, supers and standards are the same car.  The big difference is the front suspension and sheet metal . . . and the windshield and dash on the 73-79.