Ok, so here's the story. A few days back I was installing the ALTA CAI (no silicon) in my car. As part of the steps it has you have to remove the wires from the ecu. I pushed the wire cluster closer to the passenger compartment up and saw a small puff of smoke, no clue where it came from, I kept working. as things were knocked around, it happened again, this time I did some serious investigating. I noticed that whenver the bundle of wires would touch the metal behind it, it sparked (and sparks cause smoke). I could not SEE any break in the wires, but to be safe I wrapped it in some plastic wire-wrap, and called MINI.

Mind you, I have an 02 with 40k on the dial.

the service rep stated that if the wires are sparking it should be covered, but its a managers call, the manager has not yet answered my call, so lets all cross our fingers/knock on wood that this goes smoothly. I'm posting this to see if this happened to anyone else and just for some strategies with the dealer.