Are you sure that the carb boots are properly seated to the head & the carbs are properly seated in the boots? The tabs are supposed to face the head for a reason, I would not reverse them.
Did you check the vacuum piston rubbers (a/k/a slide diaphrams) for tears/cracks, & make sure they are seated properly?
42 pilots are on the small side for a bike with your mods and NBAD needles; I suggest that you make sure the slide rubbers are properly seated in the groove, & if so, then try two .5mm shims (1mm total) under each needle head & see if the situation improves.
Also, with the bike upright, run some clear plastic tubing from the carb bowl drain vertically up the side of the carb body, open the bowl drain screw a bit, & see where the fuel level is in the tube (with the fuel valve on or reserve, of course), relative to the bowl gasket...where exactly is each one?
