If you are asking whether you need to remap with the new pipes, maybe.
Depends on how similar the new pipes are to the old. Dynojet has a map to fit your new pipe/air cleaner configuration, and I'd say, use it! You don't need a new reflash if that's what your asking. With the PCIII, a dealer reflash is a waste of money.
I have the same combo on my Fatboy and Dynojet has a map for it.
Hope this helps.
