Anyway, I disassembled the extruder assembly, removed the defective heater cartridge, and replaced it. Since the new cartridge had new wires associated with it, I had to redo all the wire routing as well. A bit of a pain, but not too bad. In the process of reassembling the extruder assembly I discovered why I had been having trouble getting the vertical bolt in the extruder assembly to thread. Looks like it wasn't really a problem with the nut not being held tightly enough in place, but more a problem with the bolt itself. I replaced the original (top) with a spare (bottom), and it screwed in with very little difficulty. Looks like the original had some threads stripped. Whether it came that way and I didn't notice or the stripping was the result of all the fiddling I did trying to get it to tighten, I can't say.
So with the extruder assembly reassembled and the two hot ends carefully leveled relative to each other, I was finally able to do the dual-extruder calibration. This prints a series of squares with each extruder. By identifying the one where the two colors are right on top of each other, you can adjust the relative positioning setting in the firmware.
One thing I noticed while doing this is that dual extruder printing is not a trivial exercise. When an extruder is hot but not being actively used, it tends to ooze a little filament. This is a big problem when both extruders are hot but only one is being used. The ooze from the unused extruder ends up sticking to the build where it's not supposed to, messing up the print.
A little research uncovered this video that explains the issues and potential solutions nicely. It also has a cool lesson on what you can do with a new flexible filament type called Ninjaflex. Check it out. I ordered a spool, and will be trying it out over the next few weeks.
As a last step in setting up the printer, I cut some glass from a cheap picture frame I bought at Michael's. I now have this laid on top of the heated bed, so I shouldn't have to worry any more about the possibility that the bed is gradually being warped by the shrinkage of the plastic as it cools.
In addition to ordering some Ninjaflex, I also ordered some ABS. So we'll soon see how the printer deals with different filament types. I'm also strongly thinking about buying my own filament extruder so that I can make my own (and supply it to friends and school), but not sure when I'll have time to get to it.