After poking around the Reprap and mendel-parts forums for a bit, I haven't been able to find any known-good Skeinforge settings that work well with the gen6 electronics + mendel-parts build. I found http://ultimachine.com/content/mendel-notes
which seems to have a nice homing + cleaning routine, but wasn't running the extruder. While I continue to tweak all the settings myself, I'd love it if someone who has some known-good settings (*gentle nudge of mendel-parts folks nudge nudge*) that they'd be willing to share or a link to ones that already exist. Thanks!