fi2000 questions

i just bought a used styker and i believe i got a **** of deal with all the accessories that came on the bike. One **** of an upgrade coming from an 86 vulcan 750. One of the accessories happens to be the cobra fi2000 or fi2000r, the bike has on it a cobra intake and the 4 inch slip on. I was actually able to ride it for a half hr or so and noticed that when cruising that the bike does not want to be in a gear above what is actually needed IE riding in 4th but kicked it up to 5th (to keep rpms down) now i know that you will not have instant acceleration when you roll the throttle but it seemed kind of long before the bike got up and went it also seemed to be somewhat bogging when just giving it enough throttle to keep a pace. Is this normal and i am not used to it or should i tune the module? the module is set to the cobra factory settings for a slip on exhaust. anyone with the same or similar set up can help me out i would appreciate it. FYI I DID SEARCH.