Update: The bike started to run crappy again out of the blue. Same symptoms as before. It would start out OK with just a touch of a rough idle then after about 20 minutes it would run rough and even cough and spit at steady cruise at part throttle. Taking off from a standing start was a job with 2 up. Ran a couple of tanks with injector cleaner, no luck. Took it to the dealer for the recall on the idle (mapping) and had that done. He said everthing looked good and he dialed in the idle stepper motor which was off a tiny bit. Still ran rough. Better, but still rough. Brainstormed a little with the tech and he said could be bad gas, plugs, etc. I went through all the usual things like the crank sensor, tightening the coil primary wires etc., and I knew it wasn't the gas, so..... I changed the plugs even though there is only 3,500 miles on the bike, figuring what the hell do I have to lose and lo and behold, the bike runs like never before. It always seemed to run a little rough but I just thought that was because it was a three cylinder. Nope, this thing is as smooth as my CBX now (almost). Even though the bike has low miles it's nine years old. I guess the previous owner never changed the plugs.
Moral of the story, check the easy things first. I would have gladly changed the plugs for 30 bucks and a half hour of my time. Super happy about finally finding the real culprit.