First time build - Steel Frame CNC Router

[JAZZCNC]

Ok had good look and only see few things would change.

First home or limits makes no difference to how wired and you had it wrong. See pic how to wire Npn correctly.
Now if you have the switch travel with the axis and sense target you can have one switch work has home and limits for that Axis. Just few settings inside mach3.

Regards the VFD then yes it would be better run thru contactor than Relay contact.
However personally I wouldn't Kill power to VFD just sending it stop signal is enough IMO. While strictly it's safer to Kill power it's also pain in the arse waiting for VFD to power up just because you put machine in Reset mode. It's personal thing really but IME it's more trouble than it's worth and spindle being forced into stopping is safe enough at DIY level. The Controller will also drop the Spindle output so stops anyway when E-stop occurs.

Next I would control the Water pump using the VFD on board Relay. This way the pump only comes on when spindle is spinning.

Fuse sizes for drives are too large. 5A is more than enough.

Edit: Noticed on pic forgot to change input numbers but you should get the picture.