Hi there, Yes your quite right it has been a mission to get my machine running as it should, but now i can't fault it. mine is a 6040 but try the settings i've figured out.
Port 1 35000 Hz
Motor Tuning;
X Axis 320 1500 400
Y Axis 320 1500 400
Z Axis 400 1500 400
Set The step Pulse & Dir Pulse both to 5

Motor Outputs
screen shot won't upload at the moment but these are the settings i've got

X En (green Tick) 2 3 dir Low Active
y En 4 5 dir Low Active
Z En 6 7 dir Low Active

(Your pins may be different from mine)

When you start Mach3 change the feed rate from 6 to 100, this will give you 1500 mm/m rapid

Hope this helps
Kev