I had an aftermarket booster/master/combo valve system on my car that was pretty unsightly and I wanted a factory GM system instead. So I purchased all new parts to complete the system including rebuilt booster (Booster Dewey) a new master cyl., hold off valve, distribution block and brake lines. To make a long story short.....after bleeding the system i had a firm pedal until I started the engine, once started the pedal goes right to the floor! When I stop the engine and pump the brakes a couple of times the firm pedal returns. I initially thought that maybe it was a defective new master cylinder and swapped it out for my old one which I knew was good and after all that I still have the same problem. I'm now thinking there's a problem with the booster. It's gotta be the booster, right?
Did you check the booster rod to master cylinder piston clearance? It should be about .020 But not likely to cause complete loss of stroke. Have you tried with vacuum hose disconnected, and tried with fast idle to increase vacuum? Check the function of the booster. Engine off, press the pedal several times then press and hold and start the engine, the pedal should drop slightly and hold. Then take your foot off the pedal and run the car for a minute, shut the engine off and then press the pedal, slowly three or four times, you should feel it gradually lose "boost" and the pedal get firm as in non-powered brakes. Then, engine off, pull the hose from the vacuum source and put a cloth over the end of the hose and blow. The valve in the booster should not let any air past. Then "draw" and you should have no restriction. (the cloth is to keep from sucking the spiders into your mouth...)
