CNC checklist for first timer

Hi all,

I'm working on a Plywood 30x30 build (realistic cutting area 18x20). I'm currently waiting for ball screws to come in, but after I get those installed, I'm ready to start dialing everything in to make my first cuts.

I wanted to know if there was any kind of checklist that I should follow for setting up a machine so it's safe, and dialed in.... For instance, Moto setup, E-stops, LImit/Home Switches, etc.


My system:
1605 - ball screws
Nema 23 1.8 degree stepper motor
24" linear rails (with 2 bearing blocks so about 20 inches of travel on x and y axis)
I have a 6 inch slide module I'm using for my Z axis (Had to drill out my Bearing block screw holes to attach it)
The main table is a torsion box style has 3 inch dividers built into a grid system pancaked between 2 30x30 plywood sheets
The Gantry uprights are 3/4 plywood, and the beam is 6 x 3 made with 3/4 plywood, this is also a torsion style interior.


Electronics:
Nema 23 1.8 degree steppers (like I mentioned above)
Smooth Stepper ESS
C11G break out board
2x DM542T drivers (for X and Z axis, because I burnt out two in my kit hooking them up wrong)
2x CW5045 drivers (Y Axis)
48 volt powersupply
5 volt power supply
NC limit switches
E stop button
Mach 4

Now I've been messing around with the electronics testing everything, and I've gotten as far as getting motors running and assigned to axises, I've figured out the Estop to both make a hardware stop on all the outputs on the C11G and to signal Mach 4 that it's triggered. I've recently messed with a single limit switch to get it to both stop an axis and set it up to use as a homing and limit switch at the same time. Essentially, I think I got the most basic operations completed (all while I'm waiting for these mysterious ball screws to arrive).

What I haven't tackled yet is motor directions, tuning of motors, how to set up rotations per inch, how to make sure everything is square and plum (what is the best way to do this, I'm heard of tramming your spindle... any methods to help with this, or even design suggestions before I mount my spindle and drill some holes for that?).

I've also checked some tolerances with a dial indicator and I've been pleasantly surprised with the rigidness of this plywood design. with about 20lbs of force at the top corner of the gantry I have a totals of 4thousandths of run out. On the Z axis with about 20lbs of force I get about 2thousandths runout.... So I'm pretty happy for a simple setup like this.

Lastly, let's say I have everything square and cutting straight... where do I begin. Should I do some test cuts on something? Do I make a spoil board? what will get my toes wet and give me something easy to learn from?

Thanks, always helpful to do a google search and get some insight from you guys.