Exhaust temp differences, R/L
 

Since I got the bike running, I still am waiting for the midpipe to get here. So Ihavnt done any carb tuning as the left midpipe is about 60% crushed.

I have noticed that the left exhaust is noticibly hotter than the right side. So, I picked up one of those IR thermometers at the auto parts store for $30. The pics below were taken just after I got home from work and I left the bike running.

I took the first 2 pics of the outlet, then the next 2 pics straight down the exhaust.

Right side
http://i38.photobucket.com/albums/e1...e/IMGP0995.jpg

Left side
http://i38.photobucket.com/albums/e1...e/IMGP0994.jpg

Ride side
http://i38.photobucket.com/albums/e1...e/IMGP0996.jpg

Left side
http://i38.photobucket.com/albums/e1...e/IMGP0997.jpg

My old bike (98 with microns and jetting) did the exact same thing. One side you could put your hand in front of and the other one was way to hot to. I just chalked it up to one side of the exhaust coming from the rear head which would be closer and have less time to cool down.

Its a 2 into 1 into 2 system. If it was 2 pipes straight from the heads, a hotter side would indicate a lean mixture. A crushed midpipe is not good as it would cause backpresssure. But the only way to tell if one cylinder was running lean, or rich for that matter, would be to measure the temperature at the header pipe close to the cylinder head. Lean would be hotter. Rich would be cooler.
Otherwise just fix the crushed section, its hurting performance.

This is normal. The right side header has a restriction in it. I've ground mine out (on both headers) and it equalizes the temps. Some say it's there for a reason and you should not change it. I think that's bullshit. If you're going aftermarket and rejetting anyway then why not. Besides, it's obvious the flow is unequal.

Oh, search "restriction" and you'll find all kinds of threads on it.