Problem solved. I left out one detail, because I never set my Y stepper so high I was concerned with how it crept up and swapped it with my E2 stepper which isn't in use. Turns out the E2 stepper (formerly Y stepper) didn't get seated all the way down. Turns out if you don't have a stepper motor connected to E2 (even if you're not using it) g29 will pretend to level but not actually level!
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