Datafusions' ball(ball()) again, in creepy fleshtone:
I can confirm that the PID settings work as advertised:
P: 11
I: 0.35
D: 110
Heat up time to 220C is 9 minutes, stablized at ±4C within 12 minutes.

Datafusions' ball(ball()) again, in creepy fleshtone:

I then set about learning to calibrate the Z axis and learned a good deal about replicatorG, various calibration parts and skeinforge settings. It seems that simply setting the "carve" to 0.39 or 0.40 has reduced or resolved the issue. Each Cupcake is somewhat unique, so YMMV. I created a single walled, open, 10 & 20mm stairstep part as my own calibration piece and I'll have to upload it to thingiverse, soon. Note: Uploaded here.


Minor Improvement 3: Bolt the thermal cape to the top of the arch using the assembly bolts, and between the two layers at the bottom of the arch assembly. The fact that the Mk5 comes with its own cape strikes me as implying that perhaps it's a superhero rather than the messiah, but I'll leave my post title as is.
After this point, I'm happy to report that the Cupcake CNC began extruding its little heart out. I still had the heater PID set for the MK4, so to compensate, I simply set the temperature target at 240C. The temperature swung down to 215-ish at times, but ABS seems to melt down to about 208 or so, so I left the temperature adjustment to another day.
Extruder Board:
Once the firmware was updated, I took apart the MK4 plastruder and installed the MK5 Drive Gear Upgrade Kit and printed a part. . .or, rather, didn't print a part or even do much more than extrude a few inches of material. After fiddling with the whole setup for a number of hours I came to the conclusion that, at least in my case, adding the MK5 drive gear made the MK4 platruder nearly unusable, rather than simply rather unreliable. I couldn't get the MK4 idler/pinch wheel to reliably hold tension against the MK5 drive gear.
At this rather frustrating point I realized that my suspicions (from the start of assembly) about the unreliability of the MK4 plastruder were confirmed. As it stood, the Cupcake CNC's Cartesian drive system was useable, reliable and precise enough for prototyping work, but the extruder system was going to require a re-design.
Before I fired up SolidWorks and Mastercam and went to work, I decided to look around at options people have been coming up with around the makersphere. I lean heavily toward metal based solutions, being that I'm a machinist and having some experience now with the stresses the device was going to have to handle. As I was looking at several excellent designs that folks are using and considering the options, lo and behold, the MK5 was released.
After considering calling up Makerbot and demanding a replacement or at minimum an upgrade price, I decided that the department could affort to subsidize their work and just went ahead and ordered the MK5 plastruder.

This nearly worked, and fortunately as I tested the fit by trying to jam the filed double idler into the pulley, the top of the pulley popped off. I removed the bearing, removed the pulley top, and refit the bearing, leaving enough space for the filed double idler. After messing with different washer configurations to get the idler to sit in the newly expanded pulley, everything came together.
I was considering various options to improve the grip of the drive pulley and happened across a reference to the MakerBot site, where the problem is addressed. I've ordered the Mk5 Drive Gear Upgrade Kit, which should feed filament better and have less issues with the double idler setup, if I'm eyeballing it right. To tell the truth, I'm a little annoyed that this upgrade wasn't automatically included in the purchase, or I wasn't somehow notified that it was really, really likely I was going to want to spend an extra $10 on it. . .which I would have gladly done.
So, after re-assembly, the Plastruder Mk4.1 is working as well as it is likely to, which is to say that it regularly strips a bite out of the filament whenever there is back pressure on the extrusion due to the nozzle being too close to the part, for any of a good number of common reasons. The filament then stops feeding, ruining the part and requiring the operator to back the filament completely out, cut to a virgin section, feed it back in, test the extrusion, then restart the part. Hopefully the Mk5 upgrade will help with this.
The full photo album of the build is here.
X & Y stages assembled
Z stage leveling
Everything assembled!
Opus 1: "Don't Eat the Cotton Candy"
Summer aligning the first print
First Print: Cid's shot glass. . .well, at least a third of it printed.