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Sounds like you have a vacuum leak somewhere. But I would first pull the carb and give it a complete cleaning inside and out. You may want to replace all the jets as well. If you can't do this yourself send it out to a quality rebuilder. Then see what happens.
That was one problem, a vacuum leak was discovered when my wrench was replacing engine mounts and isolator. It runs better, holds an idle very well, but I have excessive vibrations once off idle. It seems to jump more at idle than I remember it, but nothing terrible like when at speed. The vibes are worse at certain RPMs and never smooth out. The bike is very uncomfortable to ride at this point.
I've checked compression and I have 151 psi on front, 149psi on rear. The bike starts well, has good power off the line, and at speed. Plugs look good.
I'm at a loss. The symptoms seem to have been gradual over the last 5-8 thousand miles. I recently had the timing chain replaced too. Sprockets were checked and verified OK. Not sure where to look next.
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Here is a link to an article written by Joe Minton. He wrote the book on the HSR carb... literally. He wrote the tuning guide (which is available in PDF format on Mikuni's website.)
He states that the carbs come a bit rich. He recommends a 17.5 idle jet, a #98 needle (which is slightly leaner than the 97), and a #50 accelerator pump. He says the stock main jet is usually correct (160 I believe?). There is a kit that can be purchased from Fox Distrubuting. I believe the number is in the article. I just ordered the kit from them a while back and they were really great to work with. The person I spoke to really understood the Mik carb as well.
Joe Minton was a selling a PAT (pass a truck) kit for touring bikes. It came with a mikuni jetted as mentioned, an andrews ev13 equivelant and a set of slip on mufflers. It was designed for an 80" evo. If you talk to the people a Mikuni, they will tell you the new carbs are jetted pretty close to what most people will need. They will also tell you that the 70 accelerator pump jet is on the rich side, so many drop down to a 60.
