Corey,
When I replaced the two main lines that run to the rear, I had exactly the same problem. When all the fluid ran out of the system, it took sediment that was in the bottem of the master cylinder, past the seals. When I refilled and started bleeding the system, I found I couldn't get any pressure to build up. After replacing the MC, I had no problem bleeding the rest of the system. You should check your MC for worn seals and rebuild if need be.

-Chris

'88 EFI Xtracab, 32 x 11.50 Buckshots, AZ bed, Turbo drivetrain.