Congrats ! good for you, I'm sure you'll love it.
We've all made bad calls or things we'd have done differently in hindsight, but it sounds like you did OK. I too bought my Box impulsively so know the mindset combined with the dealer rigamarole is a dangerous mix.
I would agree on the dealer's comment regarding the base, but I'm sure every S owner will disagree...whatever works for you. I'm guessing that the dealer's motive was somewhat ulterior in that there seems to be a boatload more base models than S's sitting on SoCal dealer lots at the moment, more so than usual. I routinely check out dealer inventory in our area when I'm bored, or thinking I might see an unusual color or option combination.
You can get the windstop installed post-purchase (it does make a difference), but not the Bose. S comes with a couple more speakers than the base, but I don't have personal experience listening to your Sound Package Plus.
S model is to get the 3.4 for '07, but don't let that get you down
The only other option I would have investigated would be purchasing an '05 S, which some dealers still have in inventory and are offering sizable incentives on, but you should have no regrets.