I noticed from text I shared with you that both X and Y were homed according to M119, even though I only homed X. Sure enough I got a couple different results with the M119 command from a couple of cycles of running it before homing, only one axis homed and both axes homed.
I decided to get the old multimeter out and sure enough, there was a varying voltage difference between multiple grounds as a result of poor wiring. After a quick and dirty shorting of all grounds, the endstops work just fine.
Guess it's one of the perks of inheriting a project...