I have the same machine. A couple of things. I have recently done a batch run like what you're wanting to do. I did it by marking my vice with a bit of white electrical tape and eyeballing the edge of the stock up to it, drilled all the holes with the same drill bit (smallest hole size, the larger holes I opened it manually with a cordless whilst the next part was on the machine) on the vice then moved them over to a fixture plate for profiling, located by two dowels after reaming two of the holes by hand, then ran the profile paths, chamfer, flip, chamfer.

If you are touching the home switches at any point, don't. They are lousy and will introduce anywhere between 0.04 to 0.32 error on each axis. The machine itself isn't so awfully bad at repeatability, there is a bit of backlash in mine but it ran the ops on all 6 of the parts I made without any major visual error. I chucked up my dti between each tool change and rezeroed off the reamed hole on my bed I use as a reference just to be sure but it was probably a waste of time.

To step jog, press tab on your keyboard in mach3 and you can change between continuous jog mode and step jog, and also change the step value. Spinning a dti in a reamed hole to find zero I use 0.01mm step and I'm normally back out the hole and putting a tool in within a minute.

Tool changing is the enemy. My z setter is nuts for some reason and will never give close to the same result twice so I've been z setting with a feeler gauge for awhile, takes a little longer but it's absolutely on point. Cleaning the spindle taper, spindle threads and collet nut between each tool change is also a real bastard (I've just ordered a second collet nut so I have one clean with the tool mounted ready to screw in). And also spend far too much time making sure I have the mist nozzles pointing in the right place.