Actually my problem is the exact opposite as yours. I have a GG&G A2 rear sight and a Troy Industries front sight. Even with the front sight post as low as it goes, my gun shoots about a foot low at 100 yards (and it's not me, I had a nice group of about 20 shots about a foot below my POA and another group dead center with my EOTech).
When I took off the sights, the GG&G rear was about 1/4" lower than the Troy front and the rear aperture did not line up with the middle of semi-circle of the Troy front.
I called up both Troy and GG&G and although they were very professional and offered to replace the sights at no cost (Troy even offered to cover the difference between their rear sight and the GG&G, I was very impressed), I still am not sure what the problem is. The only conclusion I have come to so far is that one of my sights is out of spec, maybe a bad forging. That's why I want to figure out the heights of the front and rear sights so I can have a better idea if one of my sights is out of spec.
Thanks in advance.