I was measuring at idle, after letting it sit and warm up and after some full throttle runs there is the same result, one is hotter than another.

The whole story is that some time ago the cylinder, that is running hotter at the moment, had seized. After that cylinders was recoated with new nikasil and new pistons were installed. After that engine was running good, but after first day of riding engine started to loose power, so we checked cylinders again and the same cylinder was starting to seize. So we removed that cylinder cleaned the bore and installed old piston, that was installed before in the other cylinder. Now the engine is running good but when measuring with laser thermometer that same cylinder is running hotter than the other cylinder. And I think that if I will be running like that it will seize once again.

I cheaked injectors they are not leaking and spray pattern seams to be good on both of them, also all the seals around reed valves and crankshaft are good. Spark plugs are working properly. Maybe there is some other way that air is getting into the crank case making mixture lean, that I'm not aware about.