After three months experience commuting from Novato to SF and back, I have transformed my 1098R into what I believe is the ultimate California superbike:
It was immediately obvious that the stock windscreen was inadequate. Most of my commute is in stop-and-start traffic, and since only maniacs lanesplit, I spend the majority of my time bolt upright and not at all covered by the original windscreen. Of course, long ago I had the foresight to stock up on several dozen samples of Craig Vetter's excellent Windjammer innovation, and have been installing them on every bike I've owned since the late 70's. My 1098R is vastly improved by the addition of a Windjammer, and I recommend every 1098 owner follow my example, since it makes every trip to the grocery store a haven from wind and debris. Once you drill through the stock fairings, there are plenty of mounting points, and because the Windjammer is so spacious, you can drill with abandon knowing the Vetter fairing will cover numerous errors.
The original tires suck, of course. Whatever they're made of, they wear out in only 1500 miles or so. I sensibly replaced them with a set of skins from Cheng Shin, and have dramatically improved their durability, and if I say so myself, their handling. A previously twitchy steed, that seemed to dive into every turn, is now rock-solid with the completely flat profiles on the C-S's. If it weren't for the extra-wide Pro-Taper bars I mounted above the triple clamps, I probably wouldn't have enough leverage to even start a turn. Rubber mounts also help smooth out the annoying twin cylinder vibrations, and the extra 8 inches in height keep my back from protesting the bike's horrible ergonomics. I don't know who Ducati thought would ride their bikes, but it certainly wasn't an American 40-something systems manager with a few extra pounds.
Gas mileage isn't what it should be, but the old hardcore biker's trick of disconnecting the spark plug on one of the two cylinders dramatically improves fuel efficiency. Throttle roll on is a little balky, but it's worth it to "go green." Best of all, I found that both Sparkys I installed on the ignition lines still flash, even when one of them isn't actually attached to anything. They make a great contrast to the neon tubes I mounted inside the fairings, to show off "how I roll."
This may surprise new buyers, but many modern sportbikes don't have enough storage space for your helmet, lunch, a laptop, boots and your Aerostitch. The 1098R is no exception (boo Ducati!) but fortunately their fellow Italians at Givi have a simple answer with their universal-mount 300 liter tail hard case. It has the added advantage of working as a backrest since it completely covers the tail area.
Of course, that assumes you've added forward controls to move the footpegs and levers to the front of the engine area since the original pegs are far too high and rearset for gentlemen of my age and deportment. A monkey will never have the salary to buy a Ducati, so why do they assume a monkey might be riding one?
I hope these simple tips help to enhance your enjoyment of what, in my experience, can be, with only a few modifications, the best sporting ride since the Virago 535.