What's the reason for swapping the interior wiring when going from a 4 spd to and auto tranny? Is it just for the neutral safety switch and the elimination of the cruise control clutch switch (don't know what it's called)? Or is there something else I'm missing? If it's just for those, I could probably keep my standard tranny interior wiring harness, couldn't I?

You would not need to change the wiring up in the front, just a couple of jumper wires should solve the problems there.
The engine harness should be changed or you will need to run several new wire runs for the start netural safety switch, reverse lights, TCC switch are some I can think of off the top of my head.