I got in here a tad late, but you seem to have it in hand. I would really suggest a master. Bypassing fluid like Mitch said.
And for knowledge, when a brake or clutch system has air in it, it WILL get better with repeated pumping up. EG, in racing, you will often see the driver pumping up the brakes and then they complain about boiling fluid. See when it boils, it creates air(gas) pockets. Pumping it up temporarily takes care of that.
Also, the master has to be bench bled before its installed. Look it up so you see how.
If not, you can get a bubble of air stuck in the perportioning valve. To get rid of this, have 2 people. person in the car, person with wrench to crack bleeder screw. First, open screw, then push firmly all the way down on pedal, not too fast, but smoothly and quickly. Hold it down, close bleeder. You should hear a distinct "click" when the damn thing resets. Do farthest away wheels in order to closest.
Also, if you must test the booster, pretty simple, just unplug the vac connection and plug it off so the engine doesn't run shitty.
Your symptoms sound hydraulic to me for sure. Could be a caliper or perp valve or other connection or leaking hose/pipe.
Really clean up each caliper, the whole thing, so if any leaks are evident they will show up. Clean em and dry them. Drive car for a day or so, make sure the master is topped up. Put it up in the air(one wheel at a time if you have to). Use a strong light and really look for leaks. This can also be done at any connection and at the perp valve.
I had this on Carmens TSi and it eluded me for several months of on-and-off repairs. Once the leak in the caliper got a bit more severe(but totally still driveable, most people wouldn't even have had a problem with it) I found the leak.