I decided to “upgrade” my generation 3 electronics to use a real stepper motor driver instead of the PWM hack non-sense.
For those who don’t already know, the Makerbot electronics are not really designed for Mendel, and specifically the extruder controller is designed to run a gearmotor instead of Mendel’s stepper motor. The Mendel firmware was “hacked” to make the gearmotor controller push 12v through a 2.3v stepper motor but, by making the gearmotor controllers simulate PWM output (which reduces the output power) it doesn’t blow the stepper. From the perspective of re-purposing existing electronics, the idea is a “really neat hack”, and in theory it should just work. Needless to say that in practice, in my experience, the extruder controller makes the stepper run hot, and with a high pitched squeak coming out of it at all times.
Re-wiring the motherboard to use a separate extruder is quite a simple task, just connect the SCL output of the motherboard to the Dir pin of the stepper driver, and the SDA output to the Step pin. However when I came to do this myself I didn’t have and couldn’t find this vital bit of information. So using a multimeter connected to the powered up motherboard I tried to determine which output should be connected to which. Well in the process of probing around I managed to short +5v to GND. I heard a fssssszt noise and saw a flash come from the motherboard….oh no!
Well I think I managed a lucky escape, one of the tracks on the Motherboard had acted as a fuse and blew, so with the bit of repair shown above circled in green, the motherboard was working again.
Giles Bathgate 
I’m using a stepper controller for the extruder as well. I took a picture of the connections, see here
I should have looked harder for that vital bit of information, and I would have saved myself a headache. I notice you also connect the signal gnd. I should probably do the same as I am currently just relying on the gnd from the power source.
With a bit of tuning, and some gearing, the extruder controller works pretty well as a stepper driver – I’ve got two of them running now, and have printed a Mendel with them. The trick is to set the PWM low enough that you don’t cook your steppers – it’s not like we’re trying to drive the extruder stepper anywhere near it’s top speed (where a proper stepper driver would really help). You can also crank up the PWM frequency if the 1 kHz noise gets to you – there’s some notes in the firmware code about how to do it, although they are a bit confusing.
Using a Nema17 stepper for the extruder is pretty overkill though – we should probably be using much higher gearing and a much smaller stepper, to keep the weight and cost down. But for now it works.
Wade
Thanks wade, I agree that the extruder controller can be used to drive a stepper, but for me its like using a hammer to put in a screw. It works, and in some cases it can be better, it all comes down to personal preference in the end. In general I feel that the makerbot electronics will be superseeded by electronics that are more readily available such as the Arduino Mega and Pololu combination
Once OverlapStrap is running on belts, the first parts Intend to build are parts for your “Wades” extruder