The air injection system does nothing one way or the other to engine run-in. It squirts some fresh air into the exhaust system just outside the exhaust valve to light off any unburnt fuel that may be there. Of course, this makes the exhaust a bit hotter and heat is what blues the pipes.
I followed the run-in instructions in the owners manual and have had no problems in 4 years. The book says to not exceed 75% max speed (you can go 80 in top gear), no wide open acceleration and don't hold a constant speed any more than you can help for the first 500 miles. For the second 500, ease the bike up to the rev limit once in a while, don't run WFO and, again, vary the speed.
