MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
I am way short with my tuning of steps/mm then and I do believe that inverting the Nimble changes the sign of the actions.
My heater block is pointing at the E3D fan the same as your's. Not sure why my heater block was close enough to melt and weld the block to the bottom of the E3D fan mount and your's doesn't. The only variables I can see is the assembly of the E3D block to the heatsink being shorter on mine or something different in the Piezo-20's size or assembly (both I had assembled by the manufacturers).
You are of course right, the shell holding the male pins is 2+mm wider in both the X and Y directions. And how stupid that I didn't think to test fit both the male and female shells before soldering all my pins. I've made my mistake, now I'll have to live with it (although my mount may be easier to disassemble than squeezing a Molex connector to get it out of the hole of a printed part)
The new board is on the way and I'll try to put a new connector on the old one to use in a different printer. Worst case, I make a micro SD image all tuned up to stick in the old one.