Did you get anywhere with this?
I have the version with the JPM motherboard which has the IO built-in (that drives the bulbs, buttons and coin mech/hopper) but I suspect for you, with the Gigabyte board (which has the IO on an ISA card), it would be possible to upgrade. You would just have to find the fastest board that still has an ISA slot and also find a way to get the motherboard drivers installed on the custom Win95 the JPM Proteus runs on (yes its Win95 not Linux, sadly), which is tricky as it does not let you execute .exe installers, it will only install via the hardware wizard (drivers with .inf files).
I did manage to get a SB Live working on mine though as the onboard sound chip had broken, which is why I think it might be doable.
Also, the problem with hacking the mech is it would not longer be easy to boot the original software. Ideally we need to figure out how the IO card works.