4 years ago, I noticed that the Mistral decal on my left muffler was much more faded than the right. Thinking it might be heat related, I started feeling the "tailpipes" after riding. The right side I could touch for 2 or 3 seconds before becoming painful, but the left side was really hot. I couldn't hold my fingers on it at all. So, I bought a Carbtune Pro and balanced the throttle bodies. No change. Next I bought a Power Commander and installed a map from their website for stock airbox, stock crossover and Mistral Cans, which was my setup. No change. Then I bought an infrared thermometer to see just how much hotter the left cylinder was than the right. Surprisingly, they were about the same. The big temp difference was only at the aft portion of the exhaust system.
I had read on these forums accounts of owners who cut apart the stock crossover, and found inside a baffle plate and some sort of wire wool, as it also functions as a pre-muffler. Thinking that something was amiss in the guts of mine, I replaced it with a Mistral crossover, and changed the PC map accordingly. Now the temp of the tailpipes are the same, and much cooler. Even after a long ride, I can now hold my fingers on both sides indefinitely without getting burned.
It seems likely to me that something inside the stock crossover shifted to cause uneven flow through it. All along, the bike ran well. Its louder now, with the Mistral crossover, and maybe a bit torquier at the lower revs. Also it used to spark knock a little under sudden load at middle rpms, which has subsided.
So if others here notice that one side is much hotter than the other, it might be because of the stock crossover.
Edit: I forgot to mention above that I keep an eye on valve clearances, which I suspected initially. I run .006 & .008, same as my old BMW. I made the above changes over a period of 2 or 3 years, as money permitted. They were mostly things that I wanted to do eventually anyway, and am glad that I no longer have to worry that the left cylinder seemed to run much hotter than the right.