I've been having some of the same problems on my tracker since i disconnected the ABS.
I removed the ABS log under the MC and re-connected the lines. Sometimes the pedal is fine othertimes it's soft or the rear brakes make a clicking sound when braking. What i plan on doing is comparing the diagrams for ABS and non-ABS and setting it up like the non system
and re-bleeding. If you look at the lines coming off the master,they come off in different locations for abs and non-abs.