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What are the possible issues with excessive pedal travel, calipers are new; low fluid, air in lines, or power booster? Does the power unit use vacumm? I'm think I may be losing vacumm, but not sure.
My first guess would be air in the lines. A second guess might be the master cylinder itself. I wouldn't think the power booster would be the problem since you should be able to get good petal even without the engine running.