I switched the sight apertures on my carry handle and A.R.M.S. #40 BUIS.

On each I punched out the pin, removed the knob, unscrewed the screw, removed the aperture, placed other aperture, rethreaded it on screw, replaced the knob and punched back in the roll pin.  When I finished both aperatures were all the way to one side and I simply used the R-L knob to get them back to approximate center.

Is this all there is to it besides zeroing on a rifle.  I'm afraid there's some other calibration I skipped that needs done.  

The reason I ask is that I'm thinking about selling the BUIS and I want to make sure I put it together correctly before I offer to sell it.  

Heres what I did. I made sure the roll pin was exactly horizontal..that is..pointing along the same plane as the barrel when I put the rear sight at mechanical zero. Doing it this way is a fail safe way to determine mechanical zero. Just lining up the lines on the 0-2 aperature isnt enought for me. This way, if your lines are aligned, and the roll pin is exactly horizontal..you know your back to mechanical zero.

I removed and the later replaced the small aperature on my 40-L in the same manner as you described. All I did afterwards was head to the range and re-zero. You did it right......