Were you getting issues? with the machine's performance before you noticed the tables were not coplanar?

Are you only concerned with the tables in relation to the cutterhead, and each other table? Or are we also dealing with a rise or sagging of one or more of the tables at the ends of each table

I ask this because the tolerances to achieve excellent cuts is probably a lot more than you would first think. Most tables are not absolutely perfectly aligned, due to very slight warps in the castings, yet the machines manage to be able to produce flat and true board faces.

As you have already started to tinker, its quite possible you are in already chasing your tail trying to attain unobtainable precision. Hope I will be able to help when I understand your situation a bit better. I am confident you will be able to get optimal performance, unless there is a serious manufacturing error, or post production damage.

Hamish.