I am struggling with your description but it sounds like what I went thru with my '93 VF 0. I fixed it with very careful leveling of the table and shimming the spindle. I did not have a way of checking my Z squareness but did find a dip in center on Y axis with careful leveling. I had a very nice level and 0.0001" indicator. 1" gageblock and a stout indicator arm. And patience, lots of that.
With the level in center of the table along X I mapped in nine positions. Shifted to Y and repeated. Slow and deliberate It took over two hours. What I found was a dip in the center along Y axis. By carefully tightening the middle two feet I got the dip out. Next I removed the spindle and the ugly shims that were there, cleaned and reassembled. I was careful to torque the bolts equal and in a star pattern. At about a 5" radius I checked the tram of the head. I mapped it in eight positions. I don't recall the values but there was a WTF moment. I did some trig... I lie. I sketched in CAD a vertical line. Drew a circle the bolt pattern diameter at the top another circle at the table distance and approximate diameter of the indicator sweep.
Taking the three points from the sweep data I made three points X,Y,Z to create an as found circle. I chose three bolt holes, front, left and right then made three corresponding points at the ideal circle. Zooming in and making a vertical line thru the point. I got an approximate shim thickness. I made U shaped shims that were as close to what needed to fix. Loosened and inserted two shims where needed. To my surprise and delight I only needed to make two retries. to my dis belief I could not measure 0.0001" at any point. Tried table in nine positions, torqued all bolts and rechecked. Still good, I could not believe it myself.
I faced a 10" square aluminum plate and it was beautiful. I have been all thru the thrust bearings on this old girl, set the backlash parameters.. actually lower than original. She does great work and no evidence of out of square.
So my suggestion is, do a very careful level and tram, might just fix the issue.