One of the more common complaints with the stock bikes is the lag in throttle response. Normally, the map from Fullsac corrects that issue to some extent. I assume you are sure that the O2 sensors are tightened, and did not get crossed up during the install? No exhaust leaks? No intake leaks? My bike runs great with the canned map and I live in Alabama, which is not significantly different than Michigan in altitude, etc. Besides, the ECM adapts to those changes, pump fuel differences, etc.
You should be able to take a bike tuned in Florida and ride it to Pikes Peak. Of course, if you put the bike on a Dyno on top of Pikes Peak, it would show different numbers, but it should RUN fine.
What kind of numbers do you expect out of an exhaust change? A 10% increase in HP/TQ is about all one can reasonably expect, so TQ in the neighborhood of 110-115 would be normal. 10% is a pretty good bang for the buck. Some people get slightly more, some slightly less. A lot depends on the Dyno and who's operating it, the weather conditions, etc.