John, if you're having the bike dynoed to tune the PC in, then I advise against doing that until you get some miles on the bike. If you're going with an already available map, then I don't think it matters much if you do it before delivery. The break-in period has a lot more to do with what you're doing with the rpm of the engine during this time and not much at all to do with the pipes, air cleaner, and program you're running (as long as it is tuned properly). Vary the rpm, don't lug the motor like ak said (keep above 2,000 rpm) and after the first 100 miles or so get a few good full-throttle 3rd gear roll-ons in up to the redline letting the engine slow you back down afterward. This will help to set the rings.