One of the original questions you asked was about difference 06-07. To my knowledge, nothing comes to mind that wouldn't be cosmetic. I've got an 07 OR with almost 100K miles on it. It's a 6spd, so similar to what you're looking for. If you plan on towing or hitting the trails constantly you'll likely have to replace the clutch more frequently than you'd like, but other than that you should be fine. I'm not a serious off-roader by any stretch, but I do get a few trips in a year (typically a few weekend trips here in the Ohio region - mostly muddy trails, rocky/muddy trails, etc) and I've hit Moab twice so far and will be heading out next year. Depending on what you want to do, I'd recommend the Xterra. In fact, if mine were to suddenly blow up, I'd be building another one up as quickly as I possibly could.
If you plan on any level of off-roading, I'd suggest that you also plan for rock sliders, skid plates, and at least a 2" lift to go with 33" tires (which will fit with a slight fix called the melt mod). Depending on your budget and timeline, you can get a decent amount of the stuff used off thenewx.org. Also, living where you do you shouldn't have too much of a problem finding Xterra owners out there.