Here's my homebrew motherboard freshly kitted out.
The arduino sits in a reverse shield of my own design, with pin sockets either side and bridges going from one line of sockets to the other. Hard to see in the photos are some wire clips that hold onto the mounting holes to help keep it steady. It's surprisingly snug with this arrangement, barely moving even when I connect the usb plug.
The ATX connector is made simply from some tinned copper wire. I'll probably put in a proper connector when one becomes available. The 12v connector in the middle of the board is vestigial, and will be removed when I add some pins for the ATX 12v extension. Multiple 12v and ground wires are absolutely essential, considering how much current will be drawn from them, as well as the likelihood of vibration.
The jumpers near the motor controllers are connected to MS1-3 so I can change the microstep amount simply and quickly. Z needs none, extruder needs it all and I'm still undecided on how much X and Y need.
At the bottom of the board next to my MAX6675 are a pair of power mosfets for controlling the extruder heater and one other item- bed heater or fan or something. The mosfets are IRL3803s which according to my calculations can handle 16A with no heatsink and 4.5v on the gate.
The headers between the arduino and the atx connector are for the end-stops which I'm yet to make.
The bottom view shows a rat's nest of point to point wiring which I'll clean up if it proves to be problematic. Signal lines next to high frequency high current PWM lines are usually a recipe for disaster, but the motor modules are so small that I'll just have to see how I go. Twisting and decoupling helps immensely, but is by no means a magic pill.