Hi Stephane,
engine:
-Compression (pistons), cams, injector size (at least for the last Formulas)
-Chip setup
-carbon covered cans
-depending on the year of production, different cranks (late Formulas do have crank type III, earlier ones share the same with the standard 750 S)
-peak power and torque figures, resulting of the above mentioned (late Formulas had 94HP and 92Nm Torque, early Formulas someting like 92HP and 84Nm, 750 S was around 84HP and 78Nm I think)
Chassis:
-different brake discs
-gold line masters (clutch/brake)
-paioli forks with pre-load-adjuster on the Formula (there is an upgrade-kit for S and SS though)
-late Formulas had 5-spoke rims vs. 3-spoke on 750 S and earlier Formulas
other:
-Dashboard had a carbon look, at least on the late formulas
-Exhaust had a different routing on the Formula (higher front of the cans for more sportive look and more ground-clearance - as if that would be necessary...).
I think that's mainly it, but others may teach me wrong.
I think the 750 SS was a S with some minor other parts like full fairing opposite to the 750 S which is half-fairing, but I am not 100% sure.
See:
750SS
750 S
750 Formula 1st series
750 Formula 2nd Series, pre-2000 Model
750 Formula 2nd Series, 2000 Model
