Since I was continuing to have extruder problems, I decided to check my hypothesis that the drive gears in the MK5 simply didn't line up properly with the plastic. Sure enough, the teeth didn't line up at all. The Makerbot instructions I used are wrong. However, that's how I installed it. So, the intermittent behavior I saw was when the Allen bolt would occasionally catch the plastic & the gear would work for a bit. Then, it would work very poorly since plastic was against the smooth part of the gear. I'm surprised it worked at all. After reversing the drive gear and re-installing the motor with a washer on each motor bolt (for spacers so the gear lines up better) the extruder unit worked beautifully!
Once the extruder could squirt out plastic on demand via the Skeinforge's control panel, I figured it was finally time for the first test print of a calibration cube. So, I used the control panel to manually warm up the extruder to 220c (room temperature 18c). Only the default settings were used since I wanted to establish a baseline of performance.
I tried my first print from the PC. Even though the bot was at operating temperature, there was a significant delay before the print started. The bot first raises the print head to do a test extract (which you grab with tweezers). You then confirm you're ready to print. Only then does it lower the print head to start the job. The first print came out rather nice and was fascinating to watch. The extruded plastic at first was a bit wavy (seen by the raft under the cube) This was solved by adjusting the extruder knob so it pinched the plastic just a bit more.
Due to a better pinch knob setting, the second print came out much better. I tested printing the same design from SD card using the default settings. I also wanted to test that I could launch a print, then disconnect the PC. So, after launching a card print, I hit the disconnect icon in Skienforge, then shut down Linux. The print still continued and the second cube turned out even better! Not bad for an evening's work! No problems having the raft of plastic detach from the build platform either. That might be due to using blue painters tape. The tape seems to give the raft something to adhere to. It also makes part removal much easier.
The object produced did produce some small plastic bumps on the far corner of the cube, probably due to a delay in z-stage lifting. I suspect tweaking some settings might be able to make those bumps go away. If not, some fine-grit sandpaper should be able to remove those kind of defects.