I agree. The component value on the JTS is great. Full 105 and some pretty good wheels for 1300 dollars. If you can get a 2007 on clearance, even better, but I just test rode a 2008 today and loooved the handling. Pretty light too.
Before I pull the trigger though, I'm wating for the same shop to get the 2008 Jamis line in. The Nova Pro looks like a great frame, with carbon seatsays, but it is a step down component-wise.
For you I'd reccomend looking at a Jamis Aurora Elite. It's listed under touring in the Jamis 2008 catalog, but it's actually their 2007 Nova rebadged and with a few minor changes (triple crank, and the carbon fork now has eyelets for a rack). Shops may also have the 2007 Nova still in, so if you can get a deal on that, awesome. Don't count on it though. They'll either have your size or they won't.
I'd also take a look at the Tricross line by Specialized, and the Axis by Bianchi, but those two brands don't seem to be priced as well as Kona and Jamis. The Axis in particular- it costs as much or more as the Jake the Snake but has Tiagra components.
Most of all, test ride a lot and buy from a shop that offers good service. As new cyclist, this is super important. I know it was for me when I started seriously riding.
Good luck. With your budget you should be able to get a really nice, versatile bike that won't let you down.