I was faced with a similar decision, and I chose the 2006.
As for the ecu--it usually takes about 3-4 cranks to turn over--about 1-2 seconds. As others have noted, this might help the cylinders get coated with oil before the engine fires up, anyway.
I can't compare mileage with the 2007, but I get between 45-52 mpg, depending on conditions. Not bad.
The new ecu is supposedly much faster, so perhaps down the line you'd be thankful for it if you decide to change maps, etc. Worth $1000? Personal choice, I suppose. I'm a little on the cheap side, so it definitely wasn't for me.
I did test ride the 2007, and the taller bars and windscreen are nice if you want more of "tour" and less "sport". However, the 2006 bars still put you in a much more comfortable stance than a race replica. I have gone 200 miles at a clip with little discomfort, especially at highway speeds. I also think the 2006 seat is quite comfortable, but that's pretty subjective as well.
You could always try to get the bar risers and screen included in the OTD price.