Running lean with Cobra Fi2000. What gives?

Well, guys, I put my shiny new exhaust on earlier this week and now there's trouble. A little background:

I drilled my stock exhaust a bit at first, no issues there. Then I got the Fi2000 CVT, installed that. No issues there. The old butt-dyno even told me it did some good with the low-rpm lugging through town.

Next I got the Baron's BAK put on there. That was a bit disappointing. The holes in the cover plate weren't tapped properly - I had to tap them out myself. For what that thing costs, you'd figure... well, anyway, I thought it made throttle response a bit snappier through the whole range.

Now, for the bit where it turns bad. I finally got my V&H Twin Slash Staggered pipes. In black. I put them on without any issues. They look fantastic. They sound great. But the bike's performance has gone a bit strange. It misses at odd times. Weird flat spots. If I'm accelerating hard through the gears, it's got some serious oomph and no issues. If I'm just cruising at 60 in 5th, it misfires at random.

It got really bad this morning when I was putting around in 2nd gear, 30-40mph. It was stuttering so bad I thought it was going to keel over. Quite a jerky ride. So I got home this morning and checked the spark plugs, and they're very, very white.

Obviously, I've got a problem. The question is, what else should I check before I start making angry calls to Cobra?