Adam,
I can see you are not happy with where you are at this time with the Acorn, why not simply return it and go back to Mach3? I've tried to help you from the start and provide solutions for you. I'm a ROUTER guy and have retrofit a few machines with the Acorn. I want to see you succeed and learn as well. I'm learning everyday how this board and software work and I'm amazed at what it can do for the money. The very first job I did on my router paid for the the Acorn retrofit. After a couple of more jobs it paid for the entire machine that I bought used. It's been making me money ever since.
The simple fact that the Acorn does not work with Mach3 is all on you. Nowhere on the Centroid site does it say it's a break out board for Mach3, nowhere. I have no idea where you bought it from but I'll guarantee it doesn't say on that website (be it Amazon or eBay or wherever) that it works with Mach3 either. Why on earth would you want to use "hobby grade" software that hasn't been updated since probably the 90's? We simply need to move past that argument because that's on you for assuming that the Acorn worked with other software.
You can slave your axis on one output, we've been over this also and told you how to do it. There are 2 ways to do it.
You don't need to used that large of a breakout board. On my first build I simply used a DB25 connector and soldered 6 wires to it. I only have 3 axis on my router. I have dozens of them laying around and can solder small things very easily. This is all you need if you have the ability to solder small wires on to a DB25. This will save you on your space issue. Looking at your photo the Acorn board could be moved to the right anyway. You dont want it too close to the VDF as they are noisy.
For your build, you need to solder 8 wires on this connector and you are done. It'll stick out from the board about maybe 20mm at the most. If you are going to hardware pair two axis then you only need 6 wires. I'd recommend the software paring over the hardware paring but you need to buy the license for the software. And to remind you again Mach3 has a license fee also, it's not free. It works in a "demo mode" just like CNC12 does and is limited in what the "free" version can do.
Are some of the pics on the Centroid site confusing, yes, and they need to be addressed but I don't work there. You are certainly not the first person to come on this forum and wonder why their stepper drives don't work on the Acorn headers as shown in pics on the website. Then everyone is surprised that they need to buy yet another piece of hardware (DB25 break out board) just to get their motors running. I hope Centroid corrects this one day.
I'm here to help in anyway I can but you have to listen to what people on here are telling you as like you said, we've all learned too and want to share our knowledge. That's why we are here. If you want help I'm here, if you want to simply give up and go another route, no hard feeling from me.