Yes, thats correct regarding enables, when you take Mach out of reset the enables go active.
Hood

Yes that pdf is giving you the initial setup steps. If the otors are the same voltage and current and the tachs are the same voltage per thousand RPM then you may not need to tune.

Regarding the DAC, no it should offset for you when you press that, or at least I think it does but you should not be trying to do an auto tune at the same time, just in case thats what you were doing.
Hood

The motors are slightly different voltage, some are 140, 142 and 145. Would is be easier to refit my old motors and buy more of the amt 103 encoders?

if the voltage, current  and rpm are close it should be ok.
Hood

ok, I've connected the outputs to the relays of each of my axis, I've only enabled the y axis at the moment (one step at a time)

I try the autotuning, but each time the kVff gets to above ~59 - 60 the breaker trips each time,

You could trying increasing it as long as it is not higher than your drives or motors can handle.
Hood

Just looked at your motor tuning, it is very low for Velocity and acceleration, maybe try increasing them.
Hood

Sorry to be lame hood, which boxes are they? and what values should I start with?? is this still on the PID Tuning (auto tuning) screen?

In Machs Motor Tuning.
Not sure what the RPM of the motors will be, it wil depend on the voltage you can supply them and what their voltage constant is but I would imagine you will get at least 5000mm/min for Velocity. For Accel you can start off relatively low, maybe 400 and see.
Hood

As always, thanks again for your help.
Just checked the numbers on my motors:

Max rpm is 2500
142volts
4.5nm

Would you still go with the numbers you recommend above?