To ride your bike 150 miles with no problem and then have the problem show up the next 75 miles is interesting. Did it do this while cruising? What rpm? Did it happen suddenly with no change in throttle, or did it happen when you changed throttle position or came to a stop? Does it happen with petcock at "on" and also reserve? A problem that comes and goes like this may never show itself.
Rather than spending time riding/testing, I would take that time and re-check the carbs. You said they were clean, etc, but you also said the problem started after the carbs were serviced. There are a lot of things you can do wrong or miss when doing carb work. I would focus on the moving parts like the throttle valves, the floats and float needles. The carb synch' may help. Check the throttle valves for any possible "sticking". I would also put the mixture screws back to where they were. Adjusting these richer as you said you did, is just trying to compensate for the real problem and may make it harder to find the real problem. It may help to temporarily remove the fuel filter and just run a straight line for now and see what happens. Do you have the correct size fuel line? I use 5/16".
By the way, about your mentioning your rubber boots/manifolds, if you had an intake leak, your idle would be higher than normal once warmed up. A serious leak would result in an rpm increase of 500 or more.
Well, let us know how things go.
I'm really kind of out of ideas. I would rip into those carbs.
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