Thank you for not being defensive about my suggestion.
It's up to you what you do of course but I would suggest working on breakout boards for the existing hardware and just leaving them as is, design a new board if you want but to break existing boards seems a bit futile to me.
I use a program called diptrace, I've looked at a few PCB design programs and it is by far the easiest to use I have found, it's free to use up to a certain amount of pins and very reasonably priced compared to other PCB design packages if you need the full program.
The first thing to build imho is a rack mounting panel or enclosure to mount the axo, some controls and a display in with some i/o jacks for gates/triggers and maybe the onboard ADCs and that's what I'll work on once I get the patch system I'm working on sorted out, I'll hopefully get around to working on some drawings by the end of this coming week and I'll post them.
I've made a panel already and have my Axo mounted on it. I have the jack sockets, encoders and display I just need to solder the headers on the Axo and wire it up.
I made a post with a link to the drawing of the panel and I think I might have posted some pics of it mounted in a rack case.
I'll draw up a range of panel mounting options and full and half rack enclosures and a standalone enclosure and post them hopefully in the next week or 2, you can take them and have them laser, plasma or water jet cut out of aluminium, plastic or wood or whatever you like if you like the concept.