Is it some best angle flap setting that a standard B-742 doesn't have? Or a war emergency power reserve setting on the CF-6 motors?
I can say with some authority that there is nothing special about the CF6-80C2 engines or the engine ratings on AF1. They are pretty much your stock standard CF6-80C2B1 engines (granted, probably maintained to a somewhat higher standard than most). About all you can do is turn off the (supervisory) PMCs and firewall the throttles - that'll give you some overboost, but only about 2% N1 above the max rating (there is a limiter in the hydromechanical control that prevents any more than that) (the B1 rating is basically the same as the B4 (56k) rating on the 767).
That being said, I've been on some flight tests where we were real light, and did max rated takeoffs (both 747s and 767s) - the climb rate is impressive indeed.
I believe the 747-200 was certified to 45k although I wouldn't swear to it - the 747-8 was 'only' certified to 43k (due to a change in the regulations regarding depressurization as I understand it). I don't remember the certified VMO for the civilian 747s, but I know that Boeing flight test pilots did take it to over 0.97 (I looked at data in the 0.98-0.99 range in a shallow dive).