Oof, yea I don’t know how familiar you are with machining terminology but the process you’re describing is tramming, or making the machine tram.
I’d recommend tramming X to the top of the Y modules as that’s what determines the bed flatness the best while still being easily accessible. The internal machining of the linear modules is inconsistent and results in exactly what you’re seeing - one side can be higher than the other.
Here’s how I do it:
Any 2 objects the same height will work, soup cans for instance. Loosen the mounts from X to Z on each side the first time you do this to ensure any residual stress is relieved from the joints.
Once that baseline is established, tighten everything up snug, and you can can then check the accuracy of the top of the modules by pushing X to the top again and seeing if it hits one side before the other.
If it’s slightly off then that’s probably normal. If it’s significantly off then it’s possible one of the Z towers isn’t sitting in its recessed hole in the base just right.
If you’re suspicious of the base you can verify the casting is workably flat with a straight edge. There have reports of the casting being warped which will affect other machine functions.
If you have a digital angle gauge it would be prudent to verify the Z towers are 90 degrees to the base and as perfectly parallel as possible. Here’s the measurements I have on mine for reference (all within 0.35deg of perfect, it should be quite close):
Anyways, probably more information than you need, but hopefully it helps paint a picture of which measurements are the critical ones.