In order to check for flatness and parallelism of the cut plan, I use the following method:
    1. Cut four small blocks from extruded foam (approx. 10cm*5cm*60cm).
    2. The wire is then moved to its rest position (X minimal position, wire levelling the table). To check te wire level, I move a paper sheet under the wire.
    3. The small blocks are placed at the four corners of the table.
    4. With 'Zero Arc',
        a) move approximately 1 mm up (Y displacement),
        b) horizontal move to cover the whole width (X). A slice is cut from the four blocks.
        c) At the end of the move (X maximal position), we take off the foam slices. Blocks are positionned once again. Their contact with the table is now clean, and we restart in the other direction. 
    5. At the end of the cut, we regroup the four slices together at the center of the table. Then, placing them side by side (two by two), and with the most precise instrument available in the world (the finger !), we check them for height differences. Proceed with all possible combinations (left hand front corner with right hand front corner, then left hand front corner with right hand rear corner, right hand front corner with right hand rear corner, and so on.....

As far as I am concerned, I then wedge my table, using bristol paper sheets under corners which are low. Then the whole processs is restarted until you are satisfied.
At each pass, I  check again the paper sheet under the wire in Xmax and Xmin positions.

I have also tried to cut a thin slice over the whole table width, turning the stepper motors of only a few steps over the Y axis.
Using tranparency, it is easy to notice the problems of the reference plan. On the other hand, be carefull while weighting your block. It should rest evenly over the whole table plan.