Lots of info to digest. some quick responses after pulling the carbs off this morning ...Just read through all of this and noticed a couple of points.
If there is no difference between 0 turns and 3 turns on the pilot screws, it sounds like there is nothing coming through the pilot passages. Your JET might be clean, but I don't think that PineSol is a proper solution to remove INTERNAL carb deposits in very small passages. By the way, how long was the PineSol solution in contact with the carbs?
Manifold boots should be almost as pliable as a diver's wet suit. Almost. Yeah, they can be softened a bit with wintergreen oil, but that does not fix the real problem. The only real fix is to bite the bullet and get new boots.
Valve clearances will affect the ease of starting and basic cold operation. Depending on how tight those three valves are, they should be adjusted.
Idle speed should be controlled at the carbs, not the throttle grip. Even when set properly at the carbs, if the cable is just a little too tight, idle speed will change when the handlebars are turned. There should be enough play in the cable to allow moving the bars fully lock-to-lock without changing idle speed.
Yeah, new boots might be $120 (actually, I just checked, saw them for $135), but how much fustration are you going through while denying that they might be the problem? I have worked on a couple of 550s and know that they are tight. You say you have large hands, which only compounds the problem (my hands aren't exactly 'petite', either). I would HAPPILY pay someone $120 to work on a 550 to do something that I am well-qualified to do, just to avoid going in there again. To have the luxury of spending a bit of money to fix the problem and be done all of a sudden seems to be worth it.
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1. The pinesol bath was a 50/50 mix in an ultrasonic. Carbs were in there for ~10 minutes followed by compressed air through all passages. I don't leave carbs in the bath in too long since PS can eat away at the metal. I've used this process on many other carbs and it works well.
2. the intake boots are not anywhere near a wetsuit. Biting bullet on new intake boots and other supplies today
3. Part of the supplies in #2 will be a valve cover gasket, so I'll resolve the valve clearances while I have everything apart. The tight valves are not touching, the shims&buckets still spin freely when in checking position, so maybe they are .01+ mm
4. I was adjusting the idle via the throttle cable control as a short term method since it's easier to reach than the idle screw, which I've now learned is better accessed from the right side of the bike than the left. In hindsight, the butterflies had been left slightly open (less than 1mm visual), which should not be enough to cause 4-6k rpm surge.
5. The carb-airbox boot on carb2 was not firmly clamped to carb2. It fully covered the throttle opening but the light clamp pressure probably allowed some air. Hard to say if it was the sole cause of the surge.
6. In general, the carb-airbox boots are intact, but the rubber has probably shrunken over the years since they can rotate in the airbox openings. Some silicon sealant might help.
7. As mentioned, i'll be getting the new boots. This is a cheap bike that I bought as a non-running project, so I didn't want to spend a lot up front until I had at least heard the engine run. Now that I know it's not DOA I'll be more willing to spend ... within reason.
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