Initial set up issues

Newbie here. I have put together an aluminum extrusion Anet A8 printer. It ran flawlessly in its plastic days but the extrusion frame has changed some parameters. And that z-axis stop is a b*****h to set. Im running Octopi 4.14.98-v7+ with Octoprint Version 1.3.10 and Klipper though on the bottom of the octoprint screen it says OctoPrint 1.3.10 running on OctoPi 0.16.0.

Im trying to set the z-axis using the the 0.1mm paper technique. Where should the Z-stop switch be set? I tried setting it as close to the glass bed top as possible using the bed screwws for the paper fit. However when I run the octoprint bed leveling routine the nozzle crashes into the glass and the right hand z motor keeps turning throwing the gantry out of parallel. Since these steppers are open loop there is nothing to say where it actually is like a servo system does so Im lost. What settings in the printer.cfg file do I need to change to get my printer bed leveled? I have found tons of stuff on setting up the pi wifi and cameras and such but nothing on the technique for something that seems very basic to me. No issues with the pi setup.

I think I would search the Internet for people who are talking about this and read what they're saying.

You should ask this question on https://3dprinting.stackexchange.com/