Finally some good news!
Was up at FamiLAB last night working on the MakerBot. Got pretty much everything working right, defined some temperature sensor stuff and configured the extruder controller's firmware and uploaded it.
Did some simple tests with temperature and the HeatCore, found it's working well! The temps with the thermocouple are rock solid, and the PID on the extruder does a great job. I decided to run some test extrusions just to squirt out some filament, and they're great! Coming out nice and smoothly, if a bit slow. Temps seem good, it's not burning the filament, and I went through a few start and stop, heat/cool cycles to make sure we weren't having any issues with the nozzle. Everything looks good so far!
I decided to push my luck really hard and get it to try a simple build, but the X axis just kept driving itself into the wall, and the RepRap host software seems to be buggy at best when it comes to working with Gcode files.. I need to play around with it more and figure out what it's trying to do.
I've taken the stock MakerBot electronics and used them as-is, no mods to the boards or anything. All I've done is take an extra Stepper Motor Controller from my Mendel electronics kit and hook it's step/direction up to the I2C connector on the motherboard with a 3 pin header. All that's needed for the stepper controller to operate is step, direction, enable, and ground. Enable is tied to ground so that the board is always on. Step/Dir will depend on the connector you are using coming from the stepper controller, but I'll post a small diagram a bit later. This is hooked into the extruder's stepper motor, so the motherboard actually controls the extrusion steps instead of sending that info over RS485 as MakerBot does. The extruder controller is now only used to control temperatures of the nozzle, bed, and a fan if used.
The thermocouple is attached using a Thermocouple Sensor board from MakerBot. I'm using the AD595C for higher precision, and have the thermocouple taped so that the tip rests in the thread near the end of the nozzle, not touching the HeatCore. The sensor board has three wires; Vcc, GND, and Sig. I hooked these up using a small 3-position connector that came with my Mendel electronics kit, and plugged them into the MakerBot extruder controller on A7.
The FiveD firmware has support for Thermistors, AD595 Thermocouples, and MAX6675 Thermocouples. All that's needed to do is edit configuration.h to uncomment the proper thermocouple #define line, make sure the others (such as USE_THERMISTOR) are commented, and change the #define TEMP_PIN to 7. This will set up the unit to read the AD595 from analog pin 7, and it will work just as normal. Need to be careful not to short the thermocouple wires as they're bare, and they will cause spurious readings if they're shorted. A single wrap of Kapton around the leads just behind the welded tip should be sufficient.
As far as further configuration of the FiveD software for MakerBot, I'm still trying to get it to a working fashion.. The axis can be easily calibrated using the standard method prescribed by RepRap. I used the 100mm to start though, so it would take less time to calibrate. All movements are accurate right now. I'm working on getting the home offsets correct, and hopefully being able to use the build limits as well so it doesn't try to build off the bed.
I will post more photos and perhaps a video tonight when I head back up to the lab to work more on this. Until then, here are a couple I took with my phone last night.