Good advice Ace. One expert can save you a lot of wasted time, money and frustration. It takes all of the "could be this, could be that" out of it. Speaking of which, I know the gen 1's had a habit of overheating due to one fan, and when thy did overheat the air temp sensor would sense the hotter ambient condition and lean out the bike which further overheated the bike. I never understood why the ecu would lean out a hot bike, but that's what they would do. Some people would take the air temp sensors out, plug the hole and strap the sensor to the bike outside of the air-box. This might have been just on turbo bikes, I'm not sure. This is part of that guess work that sucks. I'll bet Chuck could figure it out definitively.
If you haven't found it by now doing the simple stuff, its time to get an expert involved to find your problem, so ya don't burn unnecessary money.