Well, you're local to me, so I could help you with all the panel removal.
I wouldn't put the antenna anywhere the rack could interfere with it. I mounted mine in the roof basket on an L bracket... wire down the windshield channel, into the cab through the passenger side grommet.
I'm sure we could find a good place for your '05
Also remember to check out the Southeast Xterra Frontier Club
http://www.sxfc.org We'd love to have you come to our events!