The solution may be as simple as converting to Kadee couplers and draft gear boxes. Indeed, I suspect that the factory-installed Atlas draft gear box is your culprit.
I converted a pair of three rail versions of these (Atlas SD40s) to fixed pilots and installed Kadee 806s, and the coupler height came out exactly right with no shimming. But the Atlas draft gear box has a much thicker top panel than does a Kadee box, so had I used the Atlas set up, the coupler likely would have mounted lower. So switching to Kadees will help, if not solve, your problem. Mounting your own Kadee draft gear boxes also permits you to bring the coupler closer to the pilot. The box extends too far out on the Atlas stock two-rail SD40 models I have seen.
I used Kadee 806s (the short shank coupler) I think because it's pretty tight under the pilot (at least it was where I mounted the draft gear box) and I needed the short draft gear box. But if it will fit, the relatively new Kadee 747 with the under set shank would also raise the coupler head. But I suspect that you won't need to use that and that just getting rid of the Atlas draft gear box and going with the Kadee 743 or 806 will put your coupler in spec. (And yes, get a height gauge).
Now if I could get rid of that third rail, I'd be in business, but that ship has sailed....
Good luck,
RM