Finally the 4-pole terminal blocks arrived from digikey and I was able to complete the first version of the project. Here's a photo of the installed terminal blocks.

I found, to my dismay, that there is some pretty untenable noise on the stepper lines - both when powering up and just in general. I threw a large electrolytic capacitor on the barrel jack terminals that appears to have mitigated most of the problems. Here's the cap I installed - this greenwire hack worked fine, but I'll update the board files to accommodate a real decoupling cap soon.

Three things prevent me from marking this project "done" and recommending that others try it:

• There's still worrying noise on the stepper lines when the board powers up. Specifically, in the ten seconds that the Pro Trinket's bootloader pauses before initialization. If anyone had any advice about this, I'd be much obliged. (Should I remove the bootloader, which I don't want to do? Should I add pullup or pulldown resistors on the STEP and DIR lines to the EasyDriver?)
• The EasyDriver gets uncomfortably hot during normal use. I don't think this is out of spec, but I think my design is poor in this regard - it places the back of my hand in close contact with the stepped board. I should design an enclosure to give the user's hand some space away from this!
• The encoder PCB footprint needs to afford a better mechanical connection to the board. Right now, the encoder is just attached via the three terminals and not the two larger gripper tabs, and I worry I will eventually stress and break the encoder's tabs/

Improvements aside, I'm happy to be able to move on to getting the rest of the K40 electronics working. Still a long way to go there, though!