If the hot-end is at ~0 on the Z axis and I go to level it, as it approaches X = 0 it begins scraping along the bed, then when moving back to probe the center of the bed (after homing X to 0) it will scrape the bed again.
I want to add a glass plate but am worried this aggressive homing will smash the glass. How can I fix it? The printer auto-levels and runs Marlin.
Sounds like you need a different sensor? You have a lot of issues from the sounds of it. Also no code so cannot comment on your settings.
If it always scrapes the bed (sorry but its really unclear what is going on) then lower your sensor a bit.. Best I can give you with the provided info.