If you rebuilt the master cylinder or otherwise removed and drained it, did you bench bleed it before reinstalling? If you don't do that it can be very hard to get air out of it sometimes. Other than that, just check all the connections at the long run union (mid car on the drivers side frame rail) and the tee at the rear. Also, did you replace the soft lines in the rear? If not, you could have one with a pinhole in it, but I'd think you'd see leaking fluid if that were the case. Also make sure one of your hard line connections going into the rear wheel cylinders hasn't cross threaded or gotten otherwise buggered up. If its not threaded correctly it could cause the lines flare end to not seat completely and create a seal. Last thing, what type of fluid are you using? If silicone then it can sometimes take a looooooong time to get all the air out, especially with the longer run to the rear of the car.