You can buy a tramming tool ( a right angle device that has a dial indicator on the end.) You chuck it up in the spindle, and slowly rotate it through 360 degrees and see how much "run out" there is.. ( what is the high and the low) and adjust spindle accordingly to drive down the high and bring up the low.

I have seen people do this by mounting an allen wrench into the spindle collet, and use a caliper to make a measurement down to the spoil board in multiple places. That is the CHEAP and PRACTICAL way of doing it.

If your spoilboard is a little wonky right now- go for some good averages and make your adjustments. firm it up and just SKIM the bed again with your flattening bit, and remeasure. If it is not acceptable to you, make a second adjustment and skim the board ever-so-lightly.

Let us know if this solves your difficulties.

Monty