Start at the MC and work your way through the system. Crack the lines at the MC and push the brake peddle and see if you get fluid then go down the lines cracking the flare nut at each connection and see if you get fluid. This way you will be able to go through each part of the system and see if you have a blockage etc. Also check the push rod on the MC to see if it is actually pushing the valve in or not. I had that one time..drove myself crazy trying to figure out why I had no fluid only to find out I wasn't actually pushing the piston in. Good luck with your system.