If you want your SERK to sound better, breathe better, and run as cool as possible, then I'd suggest you stick it out with the exhaust for 2000 miles and then make your mods and put her on the Dyno. Or, I'd make the mods and do the Dyno now. The fact of the matter is, you're not going to tweak your bike without the Dyno regardless of what the guys running drag pipes may tell you. Your SERK is one expensive piece of hardware and Harleys these days aren't quite like their ol' Panhead predecessors. (God I love those bikes!) You've probably got a little more hedge factor with the closed loop injection system, but less restrictive pipes and a higher volume airbox will only contribute to heat problems, not solve them, in the event you don't utilize some type of fuel mangement. Most of what I've seen so far of The Motor Company's stock answer to this is to dump fuel at idle as an answer to heat management, which probably isn't a real efficient fix.
With all the Brothers and Sisters on this site, I'm sure someone has made mods and Dyno'ed and can offer some input as to their experience. My bottom line advice is spend the money once, and spend it in the right place.