I'm gonna cheat. My favorite modification is change in seating position which consists of lower bars, rear sets, and a Corbin seat with the lip moved back a couple of inches. I bought the bike as a dual purpose street/track ride and seem to keep modifying it more for the track. Next are some Tommaselli clip ons which may prove to be too much for the old back.
Hmmmm not enough yet but Ohlins front and rear, Brembo brakes, 28mm off-set triple clamp, Daytona motor with 17/45 gearing, TuneBoy, air filter, carbon tank and panels, 1050 front and rear wheels and swingarm, rear sets rased, my own 2'' rear can.
Now I need to start again on the 1050 but I need time.........
A smattering of Shift-tech carbon fiber (the rear hugger is great for keeping crud off the shock) and Skyking fender eliminator kit and frame sliders. My favorite mod is yet to come...Devious custom cold air intake and snorkel rerouting, custom velocity stacks, SAI removal, BMC air filter, full exhaust and tune-boy.
Have done a number that I felt were essential (plus they were fun to do). My favorite has been the addition of clipons. Some may disagree with the addition of clipons on an S3 but I swear the ride is MUCH more comfortable in this lower position. I was no fan of having my head so high in the wind and the clipons have eliminated nearly all of that uncomfortable drag. The handling is better too IMO.
I just bought some Raask bars to try out (read: play with). Will let you all know how those work out. They should offer a compromise in height between the standard bars and the clipons.
When discussing mods, the most important are the ones that address the bike's shortcomings.
In the case of the S3 1050 these have to be the mirrors, the front brakes and fuelling (cold starting).
The first can be solved by barend mirrors, Motrax, CRG, or normal Benelli.
The second issue I solved by going to a 5/8 master and dual lines.
The third by loading Waynes map, prodding the start button on a cold engine with throttle cracked open. Second start is instant.
I had the leather 'Carbon Effect' leather on my Kawasaki Corbin. In spite of taking care of seat top layer started peeling away in a couple of places and looked real bad.
Suggest you look at plain leather or vinyl.