Answers....
Sorry I missed them.
1) Can I port the runners in the REV-1 Manifold on the stock NPI heads?
YES. As long as there are the Coil-On-Plug provisions. You lay some Dykem lay-out fluid on the runner then the PI gasket on the runner. Then you use a scribe to outline the port shape. Then you need a good end mill to start the process. A CNC Makino could do it quickly. Once the port is close, you can drop back and punt and use a Dremel or Fordum to grind, shape and polish. Air tools work also.
2) Will an external polish job and power coating hurt any thing on the out side (for looks).
Polish job, no problem there. Any powerd coating or paint will retain heat in the plenum and runners. How much heat...hard to say but you can check with a infared thermogun before and after...although its too late by then.
3) Can I port the Supercharger even if it has an already S-port?
YES. Sure can, but it has to be done correctly. I recommend somebody who has experience, ports it. You want to create velocity to the inlet side of the blower. Do not just use a Dremel. Bad idea.
Porting and polishing the runners is a great idea and won't hurt anything since the runners are so short and boost builds so quickly.
A-Train