Should I rejet with this set up -- 3X3 Mod?

I'm running a Yosh (216550) with a stainless header and a Moose Dyno-Jet Stage One (MQ3109.001). The bike runs great at sea level. When running altitude last weekend (5000 to 8000 feet) I got a serious bog that felt like was coming from the primary (right after throttle). The 3X3 mod took care of this on my stock 02. Here's the question. If I open up the air box will I lean it out too much? Should I go fatter on the jet? Will adjusting the fuel mixture satisfy the problem?

if you open the air box you'll have to install richer main jet: back to the stock one (needle is different taper so acts like a much larger main than it did with stock needle). Final tuning depends on the altitude you ride at. Youll also have to turn air screw out to 2 1/2 turns.

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