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OK, didn't understand that you could now jump the starter and it would start and run OK. So...its truly a problem somewhere in the control circuit for starter activation. Sounds like its time to pull out the schematics and verify everything in that circuit.
Going back to square 1...Are you 100% sure the batteries didn't take a hit with the direct short to gnd? Have you performed KennyO's suggested battery diagnostics in post #2?