mpmd_marlin_1.1.x VS Ender-3-Pro

After you address whatever hardware problems you have, you need to run a software calibration, most easily done by flashing mpmd_marlin_1.1.x. The bed clip upgrade is intended to improve bed switch activation pressure consistency. G29 bed mesh and hardware tweaks are not a substitution for running delta calibration.

Have you tried mpmd_marlin_1.1.x firmware on the stock board? That will do as much as any mainboard swap could do for the specific issues you have mentioned, but you will eventually start hitting other hardware limitations. e.g., power supply, bed hole cover, machine alignment (for dimensional accuracy distortions), etc. You will still need to calibrate your machine (covered on the github page) for dimensional accuracy. There is no magic shortcut for that.

Upgrading the firmware to mpmd_marlin_1.1.x can remove a lot of software weirdness and it has better calibration routines. Someone else mentioned putting regular Marlin on there, but I think the one I linked has more calibration options.

All of the options for software calibration on stock firmware involve a lot of steps...tons of ways to make mistakes. mpmd_marlin_1.1.x firmware makes calibration a lot easier.

That's a great point, thank you for bringing that up. I was planning on doing the delta calibration with the script, but this would sure make things easier. I think this would also indirectly fix my issue because as I mentioned in the other thread on this post, the motion controller firmware is actually what's in charge of the USB serial communication (for example, you can see all the USB-related files in https://github.com/aegean-odyssey/mpmd_marlin_1.1.x/tree/master/stm32f0xx). I've been kind of afraid to mess with the firmware, but it looks like either way I will need to flash some new firmware to get my USB working properly with Linux. I will check it out. Thanks!

Regardless, I think your problem can be solved by going through the entire Quick-Start Guide, starting with Step 2 (calibration) and ending with using the recommended Start Gcode. That will include a memory wipe, delta calibration, bed leveling mesh, and z-offset. The recommended Start Gcode has the correct G29 P0 setting for doing a single probe to compensate for height differences (like your new nozzle).

If you are running mpmd_marlin_1.1.x, then your z-offset should not have been in your Start Gcode in the first place. If you are on that firmware, just go ahead and redo Quick-Start Steps 2-4 to recalibrate and setup firmware-specific Start Gcode.

Workarounds: For stock firmware, you can use the built-in WiFi instead of a USB connection (M503 does not work and I would only use this for calibration - not printing). For mpmd_marlin_1.1.x firmware, you can do full calibrations by just putting the gcode commands in a file, saving it as a *.gcode file, and printing it, as demonstrated in its Quick-Start Guide.

This is covered on the mpmd_marlin_1.1.x FAQs page, but here is a direct link: https://github.com/aegean-odyssey/mpmd_marlin_1.1.x/wiki/Pronterface-Tips

That's [how I did it](https://github.com/xan105/Ender-3-Pro/tree/master/Melzi#flash-with-the-isp-from-the-creality-bltouch-kit) back in the days before switching to a SKR mini.