So when the arcade computer failed, I tried a different route. I realized my main desktop computer (a Core i7-4790k) is plenty powerful to do some arcade gaming on the side. A long VGA/USB/audio cable later, and my arcade is now running directly off a VM from my desktop. This works so much better than dealing with moving games on/off a SD card, and managing more physical things. It's easy to manage the VM, snapshot it, and change the config without even touching the arcade now.
With VT-d, PCI-passthrough, and the ridiculous amount of CPU cores everything comes with that this should be a more normal thing in the future. It'd be lovely to use those new multi-Gbit wireless standards instead of a cable though...