Ok,
So a little update.
Last night determined by gr5's advice I went in hard on all set screws.
This still didn't resolve the seized Y stepper. I could move X without issue when the machine was powered off, but Y was just stuck.
I completely removed the 4 screws holding the Y stepper in place and inspected it thoroughly (Meh, it looked fine from the outside) however when I tried to turn the pulley clockwise it wouldn't move. So I tried turning counter clockwise and heard a very faint "Click" sound. the pulley was then able to move in either direction without issue. I carefully remounted the Stepper at this point making sure no wires were pinched and that the small belt was snug.
I took a deep breathe, plugged the power back in and turned it on.
No errors came up, I went into the Maintenance Menu>Advanced>Home Head
and the head homed to the back left corner without error.
I figured it was safe enough at this point to try my 40mm test cube again and so I did.
ANNNNNNND it printed flawlessly, no shifting, no extrusion problems, no grinding, no errors.
It just worked! this was the only test print I did last night, but i'm cautiously optimistic that this resolved the problem. Again, thanks to Neo and gr5 for all of your help and input!