Unfortunately, I was only able to spend about 1 hour working on the 3D printer today, so I don't have much more done.
I got the extruder barrel assembled. I should be ready to attach the barrel to the extruder, the extruder to the printer, then try printing something!
I spent some time trying to diagnose the non-functional optical end stop. I had already tried a different cable and a different stepper controller yesterday. Today I visually inspected the board, re-soldered all the joints, and verified that the LED is working and in the right way. I then powered up the both the bad end stop and a good one to compare voltages. I measured every joint on the board, and everything appears identical between the good and bad end stops. The only difference is that if I block the sensor on the good end stop, the LED turns on and the signal line goes low. On the bad end stop, nothing at all happens when I block the sensor. I'm thinking that the sensor must be bad.
I sent a message to MakerBot. I hope they'll send me a replacement.
In the mean time, this will not stop me from getting the printer up and running. I understand that it's possible to run the bot with no end stops at all, or to run with just 3 (for homing.)