I don't think there's even a contest here. 3.91s would have probably been a special order option, and you'd have been cruising at lifter pumpup speeds by the time you hit 100 MPH. There's a reason you don't see many Fords at the Pure Stock Drags; for some reason, they rarely put a total package together that ran that well on the street (I'm not a Ford-basher either; I own two).
Now today, anyone can build a really stout 351W-based engine, but even with the decent C9OE heads, the '69 Mach wasn't exactly a quick car. I'd guess, based upon even your data for the 3.91 geared Mach, that the Duster would trap about five miles per hour faster, even though it was rated at 15 fewer horsepower. In reality, the Mach was probably putting out more like 250 horsepower rather than 290.