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I am almost done. The Graphic in Overview, Hal and Axis works now.

rio.v and makefile OK.

One last issue: Warning: can not find toolchain installation in PATH: nextpnr (nextpnr-ice40)

Furthermore there is an error: loading joypad:: No module named 'fcntl'. No idea what I have to install here.

Just wanted to update, I spent many weeks verifying the wiring on the machine, and everything looked good from that standpoint. So I went back to the PID settings with a different approach, and have seemed to land on some stable settings that make the machine work correctly! The tool changer also needed some PID tuning and now seems to make all changes correctly.

Still have to set up the touch off probe and tool setter before I start making chips, but progress will be much slower with winter here

So wanted to thank everyone for offering help on this! When starting out you don't know what you don't know, and that made getting to this point difficult.