I have a 97 DR650 that I bought a couple of years ago and worked around some of the same questions you have.
I don't do any off roading per say so a low mount fender works great for me to use pavement to connect all of the dirt roads. I bought a low mount fender from the Euro DR650 RSE, fabbed up a mount to attach it to my fork brace and it's done. I don't know why, but I like the look of a low mount fender on a 21 inch wheeled dual sport. A low mount fender will likely clog more with mud so heavy off road use might be a problem.
I pulled of the stock headlight and gage cluster and mounted a Lynx fairing with an HID low beam, Halogen high, mounted a Vapor gage set up and a mount for the GPS and I am all set.
I've been very happy with the set-up and get interesting looks from people who try to figure out what kind of bike I am riding.
It's pretty funny to see the WTF??? look on peoples faces.