If you are going with a sidemount plate then I am assuming you are getting rid of the dog's ass. If so, then you NEED to lower the bike. Removing the dog's ass and leaving the bike the stock height looks terrible, IMO.
In short, I would lower the bike first and then do your sidemount.
I agree with Craig, altho i got the sidemount and Docs lights out of the way first, and in a couple of weeks, getting the shcoks cut (after i buy a new seat)
But i am also away from the bike working, so i wont even see the bike for a month or more.