1. The fluid had to go somewhere. Fix the wheel cyl and any other known leaks before going any further.
2. With a lot of air in a system, use a power bleeder. It can be a long haul to get it done manually.
3. A single pump of the pedal on a dry master cyl can damage the piston. Be sure to test for leak by and pull back the dust cover and look for seeping after the system is bled.
