Here's my current setup

K&N lunchbox
slipon exhaust
40/150 jets
I think either 0 or 1 washers under the needle
3 turns out on mixture screw

Engine idles great.  Good off-idle.  But it bogs at mid throttle around the 4-5k mark.  If I open the throttle more it seems to even out and start pulling strong again.  If I throttle up slowly I don't really notice the bog either.

I've got a similar set up. I ported my exhaust manifolds and pipes but that shouldn't make a huge difference. My jets are as follows, 40 pilot and 142.5 main. I put two skinny washers under each needle and turned the fuel mixture screw out 2.5 on one side and 2.75 on the other. I haven't done a valve shim test so that might be why the two are off a tad. Also, I drilled out both holes on each slide with a 5/32 drill bit. I had your exact problem when both fuel screws were turned out the same amount (2.5). Just be sure that your carbs are synchronized. Hope that helps.

 I noted that raising the needle by about 1mm increases it's mid range performace (at least on my bike).

I put a washer under the needle.
I tried putting the 2.5 to 3mm plastic washer (the one on the other side of the needle), on it, but it was running way too rich (gasoline smelling exhaust), and ran very rough.

a 1.5mm washer seems to be the best compromise. MPG dropped only by 2MPG (on average compared to stock), the 2.5mm washer gave a 10MPG drop.