Jeremy,
Sounds like your MC needs to bled some more, or your pushrod isn't set long enough?
If you have a spare piece of hard breakline laying around, cut about 4 inches of pipe with the fitting on one end and put that on the outlet of the master cylinder with the open end in a bottle of brake fluid, then pump away. Once you stop getting air bubbles in the bottle of fluid, replace the regular (on car) brake line and continue bleeding at the calipers. I've found that once the MC is completely bled, opening the bleed screws at the calipers and letting the fluid gravity bleed for a cuple of hours (with the cap off the reservoir) helps to preclude air getting sucked back into the MC.
HTH.
Tim