HUBBSTER...I've owned a mid-production 2006 and a early production 2005. I can confirm, based on both GT's, that the later 2006's are slightly "more refined". However, that depends on what you like. I still have the early '05 and I actually enjoy seeing the more "raw" CF in on the rear clamshell, the billeted A Arms, etc.
I can vouch for BJ Autos - which I bought my '05 from. I also know that Shelby Smith is a great guy and you certainly can't go wrong purchasing from him either.
If you're going to "drive it"...don't worry about spending the little extra to get a 500 mile car. Save the $$$ and buy one with 4k or so on it. You'll want the $$$ for "mods" anyway.
BTW - LOVE the Zonda. As well as Enzo and Bug. Not sure which I'd get if I ever achieve that level of success in my career. I think I'd own 3 FGT's and a few Italians before I stepped up to one car for that kind of dough.
Best of luck.