Have something similar going on with my build as well. You can see it during surfacing with the fly cutter. At some points of the table you will see the cutter leaving .001 ridge between passes that indicate the nod is tilting towards the front then on the other sode of the table it switches towards nod to the back.
Watching the tooling mark on the table is a dead give away not just by feel but by the look of the passes. Perfectly level spot has hard to define sweeps between one pass and the other.
I shimmed out my Y rails to have around .0005 of coplanar deviation. Guessing there is a slight twist in rails as they are attached to the X gantry.
This will be a complete pain in the ass to test for but it likely explains some of the issues I had in a previous thread.