michael, before you do this header mod, make sure you get a before/after sound clip, then post it here so we can hear the difference. I would think that plugging the crossover shouldn't lose any performance for your bike if you have straight thru pipes...there's probably little exhaust flow exchange between the headers, but the sound might improve.
Hope it works out for ya


'06 Speedmaster, Long TORS, rest is stock (for now)