Home Built CNC - Best way to dial in settings

I have a functional home built cnc machine. I have read up on settings but lack understanding or checklist to test aspects of the machine to configure linuxcnc the best for this machine. Also testing feed rates and jog / max speeds. I did a simple circle test with 5 passes .125 z drop per pass. 30 in/min as a feed speed works nice but 40 I miss y steps. Now I have an issue with the y with a very slight bend in the lead screw which I am blaming the issue limiting the speed on. Also when I try and vcarve text the z drops and loses 0. Might be a lot of things but this is why I am looking to understand testing configurations. Any resources to help with this would be great to know.

Description of my Machine.
Simple gantry X,Y,Z machine. 24V Nema 23 Motor's, 1/2 inch acme lead screws, 8:1 screw. Old Dell computer with parallel port. Mikita compact router for spindle

Any direction or help with a checklist to test from the bottom up would be great.

Adding I found the Stepper Tuning open office spreadsheet for jitter and Base Period settings. Stepper's are ST-4045-a1 200khz pulse max but looking for datasheet for them.

Attached are pictures of my setup. Shamefully I do not know the weight of the z fixture and gantry. I need to replace the y screw so when I pull it apart I will weigh the units. Also shamefully the picture of the wiring leads me to believe I have no self respect but I was leaning toward getting the cnc running and do plan to rewire it as I need to add limit switches. I understand I asked a question about specifics when I haven't done the leg work so all I can do is revisit this after I do more research. If you are wondering what the thing in the picture is, it's a vertical mount as the z axis can stick out 3ish inches from the front. I was doing finger joints for a box and was experimenting with joinery. Thanks.