Based on my experience, you may WANT to fiddle with the injection, but you certainly don't NEED to. My '03 runs fine with the CF Remus GP pipes and no other fuel or air performance mods (unles you count '02 elims). Beautiful pipes with a mellow, but deep note.
I've had the Remus for about 12K miles. If you're not blown away by the sound at first just be patient, after they break in they sound better and better.
PowerCommander couldn't be any easier to install. It just plugs inline with your fuel injection module's wiring harness. It helps if you havea notebook computer too.