A few comments to think about:
1. You mentioned that you rebuilt the carbs. So, first question: were they Keyster parts? If so, the float level must be 24mm from the gasket's mounting surface (i.e., with gasket removed), because the Keyster float valves are too stiff and cause a low bowl condition by about 2 mm. If the float valves are Honda, use 26mm instead.
2. The #3 plug in your picture (if #1 is on the right) above indicates that cylinder has a vacuum leak (i.e., if your spark plug boots are all within 500 ohms of each other). If your hoses are hard, you can either soften them with wintergreen oil and xylol overnight (50/50 mix works fine), and/or use wider hose clamps on those hoses to seal the leaks. If one leaks, it's a good bet the others do, too.
3. Bodi is right: the emulsifier air bleed holes can be opened up a little, and it really helps with ethanol-laced fuel. Drill the lower holes out to .035", try it and see how it goes, if not enough, try it at .037". The upper holes should probably not be drilled out past .033" unless you are at high altitude (>5000 feet) on a regular basis. The upper ones are usually .025" to start. HOWEVER - this mod is a 'last step' after all the other things are fixed: it will not fix the other problems.
4. Having the last baffle out on HM341 pipes will cause a flat spot at about 2500 RPM if you try to snap the throttle. Also, keep in mind: this bike has no accelerator pump (like most carb'd bikes of the era), so the throttle should not be suddenly snapped below 3500 RPM in any case, lest it drop dead lean and fall on its face: entirely normal. If you're into that sort of riding style, keep the revs on tap (like me), running steadily above 3800 RPM all the time. It keeps the plugs cleaner, improves the MPG (really!), and keeps the power readily available. You'll learn to hate it with those last baffles missing, though, as this is where the cam starts to go resonant and the pipes start to peak. The HM300 pipes are more open, so the cam peak moves upward: the resonance doesn't start until about 4500 RPM on those. (And, it's a much sweeter sound! IMO...)