Woo HOO another Aprilia man. Arnt those motors SWEEEEET! I heard a RSV mille at a bike meet the other day and they sound great from the side lines. Sounds even better than the V90 imo. V60 ftw. Ill be happy if mine makes the same monster noise that some of the RSV's ive heard do... I mean to listen to it from the side lines, someone else riding. Onboard bikes sound different. I guess it will be the same, may even be louder muha ha ha.
BTW here look on here...
http://www.apriliaforum.com/forums/index.php 
Post a pic for us.
About valve clearances dont check them as much as recomended... For some reason Aprilia went over the top on the recomended major service intervals. From what i read the majority of V990 engines get to well over 20,000 miles without them getting anywhere near out of spec and most never need doing.
The motor does make a lot of machanical noise though. Just normal
Have fun out there!