I am wondering if the are any differences between the two front sight bases and front sight post. I am really shooting high with aA-1 front sight post on a A-3 upper using a A-2 style removeable carry handle.

A1 and A2 base is the same.  The sight post on the A1 is round, and has 5 index notch.  The A2 is square, and has 4 index notch.

Seems to me that you need a taller post for the front base, something to do with the flat top upper/removeable carry handle issue.

Look at Bushmaster web site.

the A1 front sight is tapered also. the A2 square is not

I terms of dimensions they are the same, and each moves 5 MOA per rotation [assuming 20" rifle sight radius].  This breaks down to 1 moa per detent for the A1 (5 detents) and 1.25 MOA per detent for the A2 (4 detents).  As pointed out the A1 is round while the A2 is square.

Some removable handles are made to different heights (Which is why Bushmaster warns against using a Colt handle on their rifles).

Who's handle, barrel, BUIS, and flattop are you using?

Quoted: I am wondering if the are any differences between the two front sight bases and front sight post. I am really shooting high with aA-1 front sight post on a A-3 upper using a A-2 style removeable carry handle.

Is your FSB marked 'F', that is, for use with a flattop upper?