It seems modifying the Kicad files posted on Ergodox.org can be a good start but I do not have any experience with PCB design.
I have had lots of ideas of using the existing PCB, cut it here and there and place switches in new locations... I wrote them down, but have edited them away because nobody cares anyway.
Anyway, if you do edit the layout for a new run of keyboards (ErgoDox 2.0), I have a few suggestions:
* Please fix the solder hole positions for the outermost columns. There was supposed to be the option of 1-unit keys here, but switches will not fit because the solder holes are wrong.
* Don't just shift the position of the thumb clusters. Rotate them a bit also.
* Add support for 1×2 shift keys in outer/bottom corners like on the Maltron.
* If I had designed the keyboard, I would have offset the columns a bit more, especially the pinky columns.
* If possible, place all traces between main keyboard half and corresponding thumb cluster together ... with two parallel rows of soldering holes. So that if someone wants to cut away the thumb cluster and place it at an angle, he could reconnect the traces with a ribbon cable.
* Third 1×2 thumb key in each thumb cluster next to the others.
* Option of using a 1×2 key for the lowermost vertical index finger keys. You don't have to add switch positions, just avoid placing a bolt hole that would be in the way for stabilisers.
* Make the switch mounting plates 1.5 mm thick, please. Not thicker. If you have a PCB, then they don't need to be thicker -- it is only there to keep the switches from twisting.
* Peer review of the blueprints, to catch bugs like we had with with stabilisers and one-unit keys, ...
* Support for PCB-mounted Cherry stabilizers. (There should be support for them, but the PCBs don't have them... and you can't drill the holes because there are two leads is in the way. Moving them would not be a problem.)