OK, What exactly what were you "doing" to the master cylinder ? Did the battery run down before you were done "doing" the master cylinder ? What procerure did you use, Factory spec "doing" the master cylinder or shadetree work ? What fuses did you pull and replace ? Was the battery charged when the fuses were pulled and replaced ? Or were they replaced when the battery was dead ? Lets start there and do an online diagnosis the best we can.