So after reading Ben's comment on another user's blog regarding the perpendicularity of the beam exiting the final mirror, I checked my gantry for square. Fail. The extrusion of the gantry isn't square to the end plate. Worse than this is there's no way to adjust it without taking EVERYTHING apart. This along with Awesomenesser's pictures made me realize that this
needed to be addressed.
I made an order from McMaster, Mouser, a few different eBay members and Bart. I have plenty of parts inbound and my cutter is now almost completely disassembled. I'm replacing the Y axis drive with more purpose-built motor couplers and precision ground drill rod. I'm replacing the idlers with Bart's smooth idler kit. I'm adding lighting because I didn't realize it was such a cave. I'm also ordering more post-assembly nuts and slot covers from Misumi.
Once it's back in action, it should be a lot more accurate and a lot more clean looking. If Bart starts shipping Kickstarter rewards soon enough, I may replace the Y rails with MakerSlide. Most of the stuff I ordered for upgrades is coming from China so my blog won't see much action for a while.