Question: When you ride and apply the brakes, then ride a little more and reapply, does the lever seem to require any more travel or do you have to pump it to get the lever to tighten up? A warped rotor will force the pads on the warped side apart, when then requires repumping them down the next time you brake. If not, then it's not likey the rotor. Why one would be stone cold and the other one really hot is interesting to me. What it really sounds like is one of the calipers needs rebuilding as it's stuck; since it won't compress, the other side is carrying all the load.
There is a specific proceedure not found in the owners manual that Dave Moss teaches in order to ensure you center the wheel before tightening the calipers...it goes something like this:
1. Install the wheel and tighten the axle temporarily with both sets of pinch bolts loose.
2. Install the brake calipers, torque and pump the brakes till they seat. Some people apply the front brakes firmly, then tighten the caliper bolts to ensure they are centered over the rotor.
3. Torque the axle bolt using a wrench and a special tool to hold the axle.
4. Tighten and torque the right side pinch bolts.
5. Pump the front end (at the triple tree) up and down a couple of times.
6. Tighten and torque the left side pinch bolts.
This method makes sure the forks are not pinched inward while torqueing the axle and gives the proper amount of free play in the hub stack.
Comeon Tuf, post up....