I have seen this many times. If the fluid at the front calipers is running clear you are probably good there. As for the rear not flowing as much fluid, there still might be air trapped in the system, or you haven't moved the rear caliper pistons out enough to allow much fluid in the calipers.
With a helper pumping the pedal, start bleeding the rears right at the outlet of the master cylinder, then at the outlet of the combination valve, and then back at the wheels. See if that helps.
Also, activate the parking brake levers on the rear calipers and see if the parking brake mechanism moves the pads.
Lastly, test the brakes as I have described in an earlier post while the truck is jacked up off the ground.