Don't know much about Kona road bikes..and I hear good things about Jamis. For me, the Kona (full carbon frame, 105w/ ultegra RD, and Mavic wheels) is the better choice. My Roubaix has 105 all around with an Ultegra RD and it performs flawlessly. The Alex wheels as far as I've heard on the Jamis are junk..go out of true, spokes snap, etc. The Mavic Aksiums are the lower level of the line, but IMHO are a better name and probably better wheels.

If the extra $$ for the Kona is going to kill you, I think the Jamis is a fine bike as well..but there is a cool factor that I like with the Kona stuff..maybe from my heavy mountain bike days.

Good luck! I think either way you'll end up happy! If you like the shop with the Kona better, see if they won't give you a little off to cover all the accessories that you'll be buying there as you outfit the new ride...times are tough so I would think they would deal a little..even $100 or so off, or 20% off on some pedals or something? Never hurts to ask!