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Rallysnake,
I am assuming that you have a split circuit master cylinder with front and rear ports.
You may be having a problem with the internal pistons on the MC. If the internal fill port for the rear unit is covered by the piston, it will not fill and will bottom in the bore. This would give you front brakes and no rear.
As to caliper travel, the piston in the caliper will just keep being pushed out by the fluid pressure. It does not matter how thick or thin your rotors are. There is nothing to stop the piston from traveling all the way out of the bore. (Except for the pad and rotor being in the way.)
I would check the MC travel by opening a rear bleed nipple and depress the pedal. If the hardness is there, the problem is internal. If this isn't it, I do not have a clue.
Hope this helps.
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