At 5300 miles, the only service that would have been due is an oil change or two and the belts because of the time component (6K miles or 2 years).
Might as well get the 6K mile service taken care of. The stumbling issue you describe should be easily taken care of with a good base line set up, which includes setting the TPS, vacuum balance of the throttles and setting CO via the fuel trim, accessible by software only on your model, and the tweaking the air bleeds for both CO and idle speed. This should be done with the service, which at 6K miles also includes checking and setting valve lash.
This has been covered in grueling detail over the years and many here do the work themselves, but taking it to a good shop is a viable option if you understand the cost involved. It's a time consuming process and labor rates will add up.
Read this to understand what's required of the base line tune. BikeBoy.org - Ducati 4V Desmoquattro Non Linear TPS Baseline Adjustment (plus ST3)
. It's not hard at all if you're decent with a wrench and understand what you are trying to achieve with each adjustment. You will need access to the software required to get at the fuel trim adjustment, and having a means to measure CO is a definite plus, but many go at it without. There is a procedure written somewhere that helps you get close "by ear".
The other thing you may consider if you want to get the most out of those pipes is have the race map flashed on to your ECU. You may even find it is already on there, but the PO didn't bother to do a proper baseline set up.
A proper base line set up will make these bikes run like silk, even at low revs. It is a must do.
Welcome to the forum.
Ooops! Edit: Belt change is 12K miles or two years!