[SOLVED] Cutting Shapes Correctly, Axis not moving properly over long distances

Results of running $$ in UGS after Running EEPROM_CLEAR and using XLoader to push the .hex file from Open Source Design Documentation

UGS Output

$$
$0=10 (step pulse, usec)
$1=255 (step idle delay, msec)
$2=0 (step port invert mask:00000000)
$3=3 (dir port invert mask:00000011)
$4=0 (step enable invert, bool)
$5=0 (limit pins invert, bool)
$6=0 (probe pin invert, bool)
$10=3 (status report mask:00000011)
$11=0.020 (junction deviation, mm)
$12=0.002 (arc tolerance, mm)
$13=0 (report inches, bool)
$20=0 (soft limits, bool)
$21=0 (hard limits, bool)
$22=0 (homing cycle, bool)
$23=3 (homing dir invert mask:00000011)
$24=25.000 (homing feed, mm/min)
$25=750.000 (homing seek, mm/min)
$26=250 (homing debounce, msec)
$27=1.000 (homing pull-off, mm)
$100=40.000 (x, step/mm)
$101=40.000 (y, step/mm)
$102=188.947 (z, step/mm)
$110=8000.000 (x max rate, mm/min)
$111=8000.000 (y max rate, mm/min)
$112=500.000 (z max rate, mm/min)
$120=500.000 (x accel, mm/sec^2)
$121=500.000 (y accel, mm/sec^2)
$122=50.000 (z accel, mm/sec^2)
$130=290.000 (x max travel, mm)
$131=290.000 (y max travel, mm)
$132=100.000 (z max travel, mm)
ok