Put a 959/1299 seat on it, a lighter free flowing exhaust and a rapidbike evo to sort the fueling to make it smoother on the throttle. That's what I did when I used my 899 as a commuter a couple of years ago.
Have you had the suspension adjusted by a pro for your weight and style? that was a big improvement also, I ended up with new springs from and rear.
For added comfort...
1) go to a suspension shop and have them set up your suspension for the type of riding you do.
2) tank grips (tech spec snake skin or xline
3) Ducati comfort seat
4) gripper foot pegs
I have a Ducati Performance Seat for sale if you'd like. Great condition.I'm short at 5'7", so having it on usually left me on my tippy toes at stop signs. However, on my 60mi commutes (1 way) to work, it was a pretty comfy ride.
Additionally, not sure if you also may have issues with gripping the clutch lever, but if you do... I had an Oberon clutch cylinder installed, and now making shifts and holding down the lever is so much smoother and effortless. I was getting a lot of hand cramps with the OEM clutch cylinder.
I've found getting off the bike about every hour or so makes for a much more pleasant adventure. You don't have to be off very long. I usually don't even remove my helmet. Drink some water, stretch a little bit, gas up the bike, etc. These micro breaks make it much easier to ride long days, and ensure the riding will be fun. Best of all you don't have to make any changes on the bike to accommodate this behavior.
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