How are you bleeding the brakes? Longest line to the shortest.
"...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)(if you still have it)
If you do it this way and still have "soft pedal", take the MC back off and re-bench bleed it.