Just curious, but why are you running such a high tooth count countershaft sprocket?
This sounds like an engine load related problem to me. When I was actively racing my RC 1170 stroker back in 1979, I had a similar issue, and I wound up finally swapping carbs out. I'm guessing you're running around what, 10.5:1 compression? You might want to look at that cam and see if they recommend 12:1 or better compression. That was my problem. I had a wild ass cam (and later dropped the CR for an ATP turbo kit, NOT a smart idea with a wild cam, but god would it pull on the top end) with the original pistons in the kit being around that same 10.5:1, I was flowing plenty of air, but I wasn't compressing it enough under a load (I never did understand the math, but I trusted Russ Collins and Mark Roberston (omaha tuner/builder that was in a hole in the wall in Omaha at that time) and raised my CR and that fixed it. Still doesn't make sense to me 30 years later either.
The other thing you might check is to try BACKING OFF on your spark timing a bit. Lots of advance at really HIGH rpm's can actually hurt power..retarding the high rpm advance can net you a couple of HP in some cases, especially if your advance weight springs are a bit weak (giving you full advance under too much of a load..remember your gear ratios..big difference on engine load between first gear and 5th due to gearing)
I know these are long shots, but I've been racing cars and bikes since 1974, and I've found some rather unintuitive answers to rather stubborn problems I had that nobody could figure out for me.
I'm sure you hit all the bases with ensuring that jet orifices are REALLY what they are stamped as (I did find several jets in my selections that were NOT what they were marked as, so use a plug guage to verify the jets). Also, if you have a coil breaking down under load, that could have an effect. You didn't say if you had an electronic ignition or points either..dwell time under load can make a difference as well if you're running points.
I can't see increasing back pressure making the motor run any better. However, if you try reinstalling the factory filter box/filter, you might be suprised.
Other than these, I can't think of anything other than the ignition curve itself, under load, your final timing under load, and the cam hitting at six grand, right where your problem is in the top two gears. Is it possible that you aren't jetted right for precisely the rpm that the cam hits in? While we all know the circuits used under WOT, the carbs are set up for a stock cam. Could be that under load you're actually leaning out WHEN the cam hits.
The easy and expensive fix is to just turbo the motor and run a single carb or fuel injection. There was a really nice dual weber/solex manifold on ebay a week ago that went fairly cheap too.
I'm converting one of my super sports to E85, and managed to snag a set of cbr900RR carbs off a mini sprint car motor that were converted to pure alky for 50 bucks off ebay..square slide carbs at that! I may need to fab up a restrictor plate to get a better vacuum signal, but you might think about swapping over to some newer carbs too..
Dave