The layer shifting can be caused by lack of current for the Y motor, or acceleration set too high. You probably want it around 1500 mm/s/s. It looks like you get the failure on the model where you are making short fast movements in the y axis during the infill.
Funny story...I just turned the Y current down even lower and it's doing fine on even smaller faster Y movements I actually turned down the X current first trying to solve the horrible noises it was making..and that went so well I turned down Y as well. SO MUCH nicer now. I'm down to like 0.23 on the X and it's still moving fine with no issues and quieter than the Y was before when I was happy with how the Y sounded
Since the issue happened in the exact same place on both prints I'm really thinking it was an issue with the G code from slic3r. Wish I had saved it so I could have looked at it manually.
I am seriously amazed that you are getting 0.4 mm layers out of a 0.4 mm nozzle. I have never tried it. Did you adjust the extrusion width or are you letting Cura/Slic3r calculate it automatically?
Yeah, once I learned about nozzle vs. layer size that surprised me as well. Using slic3r and letting it calculate automatically. That was actually the defaults that folger suggested - but no clue why. It does MUCH better at 0.2mm but it's a lot slower since it's twice as many layers
For printer parts, I almost exclusively use ABS. PLA just doesn't do well around temperature. You may not see it right away, but the parts will soften and slowly deform which will end up producing sloppy prints.
I'm pretty sure the stock parts are PLA...and that makes me nervous. I honestly mostly plan on printing with ABS...I've only been using the PLA to get started and learn the ropes. I'm printing all the upgrade parts in PLA mostly for practice. Once I have a full set in PLA I plan on swapping over and starting to experiment with ABS and hope to re-print all the parts in ABS before I do the lead screw upgrade.
Also, Snarls you should run M119 to get the end stop status to make sure they all are reporting what you think it should be if you get problems with moving the axes.
Yes Though I have noticed that when you haven't homed it shows axes that aren't even wired up as triggered. So that confused me when I was trying to sort out my X axis mirroring!
Just got brave and did 6 parts at once for the first time. And they all seem to have come out great! 2 more pieces to print and then it's time to try ABS