Yes, dealers are buggers for trying to keep hold of original bits, fasteners etc. They probably come in handy for use on other bikes, but they're not there's they're yours, you should be getting them back. For example: The Suzuki centrestand is supplied with a much longer hero blob for the left footpeg, they may try to retain the original, ask for it if they do, it's yours.
Regarding the buffeting, just dropping your head doesn't just affect the relationship with the screen, think about the mirrors too, just raising the screen alone doesn't make much difference, fitting Aprillia Tuono mirrors will though. Do a search on here and watch the results page light up.
http://bit.ly/14FEm7G