Unless the hose connecting the two calipers on the front of the bike is clogged (highly unlikely), it is the nature of any hydraulic system to be self balancing. As pressure is applied to the brake fluid in the system, only the diameter of the pistons will have any effect on how much force is put on the individual brake pads (although a sticking seal can change this it is a relatively small consideration).
Any difference in temp. you can feel with your hands between the two front rotors is really insignificant as when the brakes are operational and being used, the surface temperatures are much, much higher than anything you could stand to touch. What I think you are feeling is just the difference in the running drag of the two sets of brakes and does not really indicate how much actual braking is being done by each rotor.
There is a certain amount of drag in disc brake systems and that along will cause a bit of increase in rotor temperature. As there is always some thickness variation and some run out in all rotors, it is that very small change as the rotor rotates that tends to push the pads back and the caliper pistons back in their respective bores. In the normal variation of things, one rotor will be less true than the other (statistically it will just work out that way) so while both may appear 'smooth', the rotor with the greater run out will push the pads back faster and a bit further, and that will reduce the friction and heat caused on that side. Same thing goes for the seals- some are tighter than others, and a tighter seal (easy boys!) will tend to hold a piston and brake pad closer to the rotor than a looser seal would.
The only way to really check on braking action would be to either install a pressure gauge on both calipers and watch them as the brakes are used (you can be stopped for this test although a moving test would be more useful) or put temp. sensors on each rotor and note the temps. the rotors achieve, again when actually being used and loaded.
Otherwise I would just assume all is within a normal range. It IS normal for some pads to wear sooner than other pads on the same caliper; mine tend to wear on the insides of the rotors faster than those on the outside of the rotors. To get maximum life out of the pads, some people swap the positions so each one gets its 'turn' in the high and low wear place.
Brian
removed calipers, disassembled and replaced all seals last week. bled brakes, (speed bleeders are my friend) including all banjo joints. pistons all seemed perfect. went for short test ride and then longer ride (50 miles to work) and the right rotor is still quite a bit warmer to the touch than the left at end of ride. I think that is telling me that the left brake is still doing more work than the right brake:( just like before, but not as bad.
I'm not sure what to do now. could the fact that the brake line goes to one brake and then loops over the tire to the other brake cause a change in brake fluid pressure to affect left and right brakes differently?
Is there anything else that might cause the application of the front brake to be unequal between the two?
Thnking maybe I should change the brake lines at the triple tree connection to two equal length lines and eliminate the crossover, but I don't want to change the lines if it won't make a difference.
any ideas?
thanks