I find the drive position quite comfortable, so I'll not change it.
No matter, if you want only raise the handle-bars you can do the spacers, but if you want furthermore pull back them, I think is easier make a new upper clamp fitting a Monster's type handle-bar, or welding two raisers on the stock upper clamp.

About the Staintune: all the open mufflers require a richer mixture, or the exhaust valves could go burnt.
On the P7 ECU there is a potentiometer to richener the mixture, but I don't know if it's enough only richener the mixture trimming it or it needs also to change the chip on the ECU.
I would also like to know it, because I have a mod chip and I'm guessing if fitting it or not with the stock mufflers.
No matter, to find out the chip, you have to open the ECU.
The stock chip has a label "Ducati 907ie -023-" on to the european bikes, or -023U- on the USA bikes.

Ciao