Sounds like the indy doesn't have the most experience with braking hydraulic systems... or doesn't have all the proper tools to diagnose it. If I'm understanding the problem correctly it most likely needs the master cylinder changed and a full fluid exchange. The replacement master cylinder would need to be bench bleed before installation just like any other car, then I'd simply compress all 4 wheel calipers to back flow fluid into the master cylinder reservoir knocking any small air pockets at the top of the lines out into the reservoir. Then use a pressure bleeder to perform a regular brake fluid flush/exchange to all new fluid. If there are no leaks and no air in the system and the job is done correctly, then the ABS system would not get any air in it and would not need to be activated in the bleed procedure.

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