Well from what you have explained...It sounds like you have a pretty big issue on hand with the surface area where the tanks are sitting not being true.
I HIGHLY suggest going down to Home Depot or Lowes and buying a 4x8 sheet of Insulation board that is used on the exterior of houses.
You can buy a 1/2" thick sheet for about $8-$10.
This will soften the imperfections of the stand and will allow your tanks to sit flat on the wood.
Btw I figured I'd let you know I most definitely took your advice. We bought a sheet of pink 1/2" insulation from HD tonight after I got off work. Had them cut there and Hope is now rescaping the first tank on the top now with the insulation under it. I wasn't sure what I was going to get while I was on my way there but once I saw the sheet and felt it I was like "oh damn that's EXACTLY what's going to solve the problem." No water, just sand and decor, and it's already not rocking and level with that insulation under it. Honestly I think if I ever build any stand for future tanks, besides not totally screwing up the measurements by using warped 2x4s, I'll use one sheet of plywood and one sheet of this insulation.