arodrigues, i just went through a similar issue. I hope you dont have the same problem. I installed a brand new ATS transmission in my truck , and had the same issue you discussed. Over time, the problem worsened and finally, I had the transmission pulled from the truck. The problem was that the transmission case itself was cracked. The vibrations initially started at high rpms, but as the crack worsened, the vibrations occured at lower and lower RPMs.
Hope this is not your problem.