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Yes, start with all the settings that’s possible to get in MesaCT, 

Spindle relay would probably be good enough for now because the mill has a gearbox and 2 speed motor but that’s possible to fix easily outside of software if necessary, 

For some reason there’s a lot of modules that’s missing and causing faults, I don’t know maybe the new changes to 2.9.4 don’t need them and the AI think they should be there and write HAL with functions that’s not supported any longer 
 

Yep, I think you normally tune the inner (velocity in this case) loop first

Yes, you will probably need to setup the MPGs manually

MesaCT should allow you to setup home/limit switches,
your coolant outputs and the Spindle control outputs
(not sure about the spindle PWM)

So I would setup the limit/home switches and various outputs
next ( since support for these is built into MesaCT )

At one point I got these pins to register counts in Halmeter:

hm2_7i95.0.inmux.00.enc0-count
hm2_7i95.0.inmux.00.enc1-count
hm2_7i95.0.inmux.00.enc2-count
hm2_7i95.0.inmux.00.enc3-count

But ended up getting errors for missing module: Motion.so so tried clean install and wiped everything,

MesaCT is a useful tool but haven’t found any encoder settings other than motor encoder setting,

I’ve tried to flash different firmwares also because some firmwares doesn’t have all settings available for encoder and spindle in MesaCT,

At the moment I’m running 7i95t_1pwmd

I think 7i95t is only supported by MesaCT, tried to use pncconfig because I’ve seen posts about people using the 7i95 config and edit I/O mapping and such, but couldn’t find the 7i95 either.