The pins connecting in the center was because you didn’t have terminals defined (without a terminal the connection is the center of the pin). Then edited the fpz and cleaned it up (tried omitting the unwanted pins in pcb view but that doesn’t seem to help). Then (after I discovered Inkscape 9.2 appears to be a bad idea!) I adjusted the box in schematic to center the pins better and added the missing terminal definitions. I also changed all the connectors from the 0 width (that are invisible in Inkscape) to. The broad outline of the changes is that I ungrouped everything in both breadboard and schematic views (many many nested unused groups) then in schematic cleaned out anything that wasn’t an in use connector or a line on the drawing (there are a bunch of unused connectors in there that don’t hurt anything necessarily but are messy). You have a variety of problems, missing terminal definitions mostly, as usual it was easier to fix them than try and explain how to fix it (although I also don’t know how to fix it so it is happy with the screw terminals).
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