Congrats on the new bike! You will love it. $8900 for an XB12 is a stellar deal IMHO.
If you want to do some research on the best exhaust/ecm/airbox setup, go to americansportbikes.com and click on the exhaust shootout link.
That is an exhaustive (pun intended) study that they just completed on each aftermarket setup for both the XB9 and XB12.
Once you get the exhaust/ecm/airbox done, well, I guess you could look into suspension stuff, but the stock suspension is great the way it is... it usually just needs some tweeking for your weight and riding preferences.
They do sell a big bore kit for the 9s, but I don't know about the 12.
I put an aftermarked handle bar setup on my cityX (XB9SX) to lower the riding position a bit.
One very important thing; If it did not come with frame pucks (black plastic pieces that are attached to the frame, just where it slopes in in front of your knees) I would HIGHLY recommend getting them. They have been proven to save the frame, and therefore your fuel cell in the event of a slide. They cost about $45 for the set. If you rub a hole in your frame into the gas tank, the bike is totaled and un-repairable.