If it was running rich it would start without having to advance the fast idle. Read up on how to do a plug chop. Take the bike up to where it is miss firing and shut her down as per the plug chop instructions. You might have to do it a couple of times to get the hang of it. Do this on a quiet road somewhere where you can push it safely to a place where you can work on i it. A back up vehicle is handy to act as a buffer. Hopefully reading the plugs after doing this will give some indication of what is going on. What exhaust are you currently running? Have you used DeoxIT on the ECU and FICU. I have just bought the new Deoxit which now comes in two cans, cleaner and a gold coating can. I had run out of the old DeoxIT of which I only had the one can of cleaner. It was given to me many year ago so I'm not sure whether I was missing a can. Even the new DeoxIT failed to fix my 4 pin fuel pump connector that had only ever had one problem in twenty years.
Regards Martin.
Sorry for the late reply Martin,
Yes, I have used Deoxit on both the ECU and FICU. This exhaust is custom-made by Iron Cobra Fabrication in Long Beach, CA. It uses a 18" Cone Engineering muffler. If you want more information on it, here is a catalog of their pre-fabricated products,
http://www.coneeng.com/pdf/motorcycle/MC-finished-Mufflers.pdf. I did a plug chop earlier, the color of the plug seemed fine. I also just install brand new NGK plug wires. As of recent after installing the new water temp sensor, the bike runs great once warm, no misfires at cruising anymore. However, it really struggles with start up, I need to turn the fuel advance up all the way and hold down the ignition button for a few seconds for it able to maintain idle.