Can you seal off the top of the master and then put a vacuum on the reservoir? Any air hiding in the system will have no choice but to go to the top.
Also if you vac it out and close the valve you can see if it will hold a vacuum. If it won't you will have found out why your pedal is spongy. Then you get the fun of figuring out which seal can hold fluid under pressure but not air from the lack of it.
