You should be able to set the ferror and min ferror much smaller
also all lines like: setp pid.?.maxerror .0005 should be commented out
You can further improve the following error by using the DPLL:
# latch stepgen position feedback 100 usec before nominal read time:
setp hm2_[HOSTMOT2](BOARD).0.dpll.01.timer-us -100
setp hm2_[HOSTMOT2](BOARD).0.stepgen.timer-number 1