You basically have to get the carbs out to do the freak anyway, you may as well re-jet then. Also, the whole point of the freak is more power, why short change it by not re-jetting? When you pull out the airbox (or hack it up with a dremel like me), and BEFORE you put in the freak brackets, that is the PERFECT time to pull the carbs and re-jet. You'll NEVER have easier access.
Also, it's one of those things that is scary to think about, but once you get started you'll kick yourself for not doing it sooner.