[dsraven]

do you have disc/disc or disc/drum? if drum rear have you adjusted the brakes first, with the park brake adjusted fully off, then adjusted the park brake properly? adjusting the brake star wheel sets the shoes against the drums on the bottom end but the park brake adjusts the shoes at the wheel cylinder end. if no park brake in place then the wheel cylinders get pulled all the way back in when the brakes are released and require more fluid to be displaced upon brake pedal application so you end up with a low pedal or a pedal that needs to be quickly pumped to get any pedal height.
have you checked to ensure the pedal and master push rods have the correct amount of free play but not too much? do you have the correct free play at the master cyl push rod from the booster? not enough play here will not allow fluid to get out to the system because the piston in the bore has not been allowed to come back far enough to expose the hole from the reservoir to the bore of the cylinder. this would require the master cyl be removed from the booster (but not the system) and a depth check of the master input bore compared to what push rod length is sticking out of the booster. a vernier caliper works good here. another way to check this is to take the cap off the master and look for a disturbance in the fluid when you initially push on the brake pedal. this is fluid pushed back into the master res upon initial pedal travel because, at rest, the piston in the bore of the master actually travels back far enough to expose the "fill" hole in the bore so fluid can return to the res as it heats up and expands or cools off and contracts in the system. then when the pedal is pushed a small amount of fluid is pushed back into the res until the pistin travels past the fill hole in the bore of the master. check any linkage wear points that may skew the actual push rod travel at the master cyl? do you have the same ratio of pedal travel as the stock set up?
if disc/disc, check to see if the pads are out against the rotors on all 4 corners after you have pumped the pedal a few times( and checked to ensure you have fluid in the reservoir between the pumps. if you pump a few times and don't check the res then check and find it is empty, you may be starting over from scratch in the bleeding department). if the calipers are off then you can use a block of wood between the calipers, where the rotor would fit, so the pistons don't get pushed out of the caliper bores.
does your master cylinder have res valves as well? they will be visible where your lines connect to the master. they are usually installed in master cylinders intended for a drum brake application in order to keep a small bit of pressure in the system so the brake cylinder cups stay sealed against the bores.

keep us posted