Well I tried my hand at modifying some firmware and such, was a bit of a bust but here it goes:
Changed the v1.8 Heated Bed firmware to support the stepper extruder and also modified some code to use a thermocouple instead of a thermistor for the extruder temp sensing. Went up to FamiLAB and tried it out.. the thermocouple worked fine, but the stepper motor would not mobe. I'm not sure what the issue was.
The unfortunate thing is that there's no mention of how to wire up a Lin Engineering stepper to an extruder controller. They use Red/Blue/Green/Black wires, and I ohmed out the stepper looking for the two coils, which I found, and hooked up to the 1A/1B/2A/2B posts on the extruder controller. Tried to enable it and the H bridges got really hot, but no motor movement. The bridges stopped outputting power after that.
Looking in the Makerbot Operators group, someone mentioned that having a stepper connected that was less than 6 ohms might cause the H bridges to burn up; the Lin Engineering ones are about 1.8 ohm. However, they're also recommended on the RepRap website as steppers to use on the extruder controller. I'm a bit confused here, how are they normally used? There's a distinct lack of documentation as to what the resistance should be across the stepper terminals, so I'm of the assumption the H bridges were bad anyway and I didn't screw up there.
However, I did manage to screw up afterwards. Some folks in the Reprap channel on freenode were trying to help me troubleshoot the problem, when I managed to find out that the extruder controller has no reverse current protection in it. Hooked the 12v up backwards and blew the H bridges on my new board. Well damn.
So I'm ordering 6 new H bridges from Digi-Key, hopefully i can just replace them and that'll fix the boards, and perhaps try again to see if it was the bridges or if the stepper is the problem.
If anyone has some insight into this, it would be much appreciated. Been an ordeal just trying to get this working..