I wouldn't worry about it too much - I chopped mine right down to get it to fit my bike as snugly as possible and there was still quite the performance gain. While I'm sure different header lengths does effect where you get the most gain, it does increase performance across the entire powerband, quite significantly in comparison to stock.
So while it would be nice to "tune" it to where you wanted the most gain, it's not like you lose gain if you hafta chop it down. I prolly cut out a total of 2" from various sections (about 1/4" at a time with test runs in between) with no perceivable loss.
o_O You have another
new motor? lol - how many does that make now? Color me jealous