Sounds like there is still air in the system. A few questions for you.
Did you bench bleed the MC?
Where did you get the MC?
Were the MC and calipers new or rebuilt where did you get them? I have had problems with brake componets bougt at places like AutoZone, Kragen places like that.
Is this how you bled your brakes?
This is the proper way to bleed your brakes to avoid spongy brakes, etc...
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"...This is from the FSM and it works great..."
1. Drivers side rear
2. Passenger side rear
3. Passenger side front
4. Drivers side front
5. LSPV (Load sensing proportioning valve) This is very important step if you still have this valve. If you do not know where this is located, it is on the PS rear mounted to the frame with a rod connected to the rear axle housing.