"The bike is an immaculate '05 with 9k on the clock, and judging by it's only previous owner, has led a very pampered existance, so I wasn't anticipating any mechanical issues."
Probably didn't have any until you changed things. That's how it works. Changes seldom go perfectly. Since it is popping after the dealer "fixed" it up with the new pipes, why not ask the dealer to fix the popping, for free. He should. The old leak may or may not be a leaking cap gasket. Just watch it and DON"T try to tighten the bolts on the top of the cam covers without knowing what you are doing. You could strip them easily.
I may be wrong, and two good mechanics above already think so, but I don't think that removal of the AI should affect the popping one way or the other, but it does make it easier to get at the plugs. There are kits you can buy or you can follow instructions in the tech blogs section on what to buy to make your own kit.
I would try adjusting the mixture screws just a hair, as has already been suggested.
If you are patient and work with your mechanic all these things are minor and should be worked out fairly easily, so do enjoy that new ride!!!
