Thanks to Mahan for pointing out the Smoothieboard 5X as a possible retrofit option. It seems most robust and has more than enough brains for the problem.
Calibration: this is where the magic happens. Luckily we have the entire Stratasys users manual updated to this project, so we can take a deep look at any wiring considerations long before we make a single cut.
we'll also need to consider how to feed material to this machine, since we're looking to bypass the microchipped cartridges altogether.
when entropy finally catches up with us and we have to improvise a homemade extruder assembly, we have an entire machine shop at our disposal to make custom parts. The only way we can dodge this bullet is with a retrofit like this, because if any pieces in the puzzle at the moment become borked, the machine sits, like it has for nearly a year.
I'd really like to get more people using this machine, and not having to fear some bozo ruining it for everyone. Even the Makerbot needs a little love, but this Stratasys is a beast, and certainly worth keeping.