Engine/Transmission (1994 - 1998) brake fluid leak

[dodge cummins]

ok changed brake pads on my 96 cummins 2500 the other day and the haynes manuel says that you are supposed to drain 3/4 of the brake fluid from master cylinder and refill with new fluid. well i filled the master cylinder up to the wet line it was before. now 2 days later i have fluid leaking from the fill case like it was overfilled and it got fluid all over everything. i pretty much washed everything down with water. today i took fluid out of the fill case. does anyone know how much i should take out or is this a sign of another problem? i filled the master cylinder with a heavy duty dot 3 from a company called gunk. it said that it has a dry boiling point of 450 degrees. also when i opened the fill case the rubber piece part of it looked like it collapsed. i open the fill case and reset the rubber piece in place but when i put the lid on it sinks back down