Are you looking at new bikes for you and your wife?
If you're going to buy two FJR's, you could always get one of each; '07 & '08.
Personally, I would save all the cash I could, and look at the '07's. If you can save a couple of grand, or more, it's the way I would go.
It took my dealer 10 minutes to change my ECU. I never had any problems with it, but Yamaha sent me the letter, so I got the new one. In any event, it's not a problem.
My tranny has never given any trouble. After 7,000 miles, the only shift that is a little clunky, is 1st-2nd, and that's smoothing out. 2nd-5th so easy there's practically no feel to the change, atall.
My oldest son got off a Road Star 1700. The change is like the difference between riding a burro, or an F-16. You'll be happier - trust me. The only problems you may have, is with ergonomics. Don't give up, if you find the riding position uncomfortable after a while (I considered it). A simple set of risers alleviated my problem, and turned my FJR into more of a long distance bike than any Star model will ever be. AND ... No more of that underpowered, anemic, thumping vibrator underneath you!
Good luck.