Answers to your questions can be found on Stoptech's web site.
Specific section on Pad and Rotor Bed-In here:
A brief summary:
1. Each time you switch pad compounds the bedding process must be repeated. The process removes the old pad material from the rotor and replaces it with material from the new compound. Which is why some prefer to change rotors as well when switching from track to street pads.
2. New rotors must have the pad material applied so yes, you must repeat the process even if the pads are used. Note: old pads on new rotors will result in very poor braking until the pads wear enough to match the rotor's new, smooth surface.
3. Brake temps are only useful if measured at peak operating temps. There are paints you can apply to the rotor to accomplish this.
4. Experience - either yours or what you can learn from others. Better brake cooling can help, as well.
There is a lot more detail in the Stoptech papers.