[mactec54]

I interpret the answers then as 2 mechanical limit switches per axis screw, (8 total), that are tied to the E-stop circuit to prevent a malfunctioning motor from causing damage and 1 inductive switch per axis for homing, 1 for x, one for y and 1 for z. The y one can be on either side, but does not need to be both.

Are the e-stop limit switches wired to the controller individually?
Should the e-stop be NC so if there is a broken wire the circuit would be open?

You only need (1) Micro switch or proximity sensor per axis just as this video shows, most modern machines where the controls have soft limits, you only need the (1) Micro Switch / Proximity sensor per axis

If you need Gantry Squaring, then you would use ( 2 ) on that axis.

Proximity Sensors are the best to use as they have better noise immunity than Micro Switches

Power EMI Filters are always needed for a system like yours, this is a Filter I recommend for new machine builds, TDK Lambda RSEN-2030L just a heads up not all Power Filters are created equal

You will not need a Breaking Resistor installed for any of your Axis Drives

Here is a video for you to look at, that may help with your wiring, is using the same control as you are using

https://www.youtube.com/watch?v=DcgBTxemPlA&t=13s