A number of guys on the cbr1100xx owners forum have replaced their stock with 4 into 1.

I helped a friend do his (Akrapovic) , and here's what I discovered:

1) The 4-1 header removes some clearance under the bike.
2) There may be no center stand stop, and some 3rd party center stand stops will won't work
3) You may want to order some extra studs and nuts for the exhaust header. They have a tendency to not come apart very nicely, and it's a pain to get the new header to seat properly using the old studs and nuts.
4) When you put the studs in, use Anti-sieze compound on them to keep the above problem from happening again.
5) Power Commanders are not necessary, the EFI will for the most part do it's job. However.. the Power Commander will usually provide a better way to tweak the settings of the EFI, and the ONLY way to tune it. Most of the downloadable maps are OK, just make sure you get the proper PC for your bird. 02 and greater require a PC3, 01 and previous EFI models require a PC2