My 1100 midnight custom did the same thing, and I did a tune up, new air filter, and then put on the new exhaust and had it rejetted by a mechanic. He synced the carbs while doing it and did all the work on a dyno. I still have that lil hiccup once in awhile.
I wouldn't worry about it, its just one of those things that happens. I beleive its better without the AIS. Just my thoughts!
Bob aka busterrm