First thoughts that come to mind are the condition/quality of the pods, the pipe, valve clearances, how clean the carbs are, how the carbs are adjusted/float levels, even the possibility of mismarked DJ mains (I know, not likely)...just trying to think of things that could limit air flow and cause you to need a little smaller mains than what is usually used for your mods.
Did you test at full throttle and chop off and read the plugs?
What were the 1/3 throttle position (jet needle) reads?
Generally, you choose the main that delivers the highest top speed under same conditions. I often do that, but, some bikes will perform well at top end but a full throttle roll on at approx' 60 in top gear may show some momentary bogging. That situation may be that the bike can't handle the overlap from jet needle to main during a roll on. If that's the case, then I always consider the jet needle more important to general riding and I test and make sure the jet needle is spot on first. Then I go up as large on the main as I can without it starting to bog again. This may be "backwards" jetting according to some sources but it has worked for me on some bikes.
Your jet needle position is what surprises me more than anything else. If you did test and get good plug reads at 1/3 throttle, again, it seems like your bike is lacking flow and it needs leaner than usual jetting. The plug reads are what's important here.
I'm not trying to cause you work, just trying to figure this bike out.
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