S&S headers are in no way too small for a top-swapped motor. 90+% of the the people with M90's do NOT need the 3" downpipe that comes with the other header options available to us, myself included. Ron is about to bust 11's with S&S headers and the stock camshaft, another member is running 114+ mph traps with his S1X/Gen 5/IC GTP. There's plenty of head room with S&S headers, and don't let anyone tell you otherwise.
I got caught up in the "OMG TOG's rock!" mentality and they hurt my bottom end a great deal when I was N/A. I picked up one mph in the 1/4 but actually lost a tenth, despite and identical 60', because the car was so soft at the bottom of the gears.
My opinion:
Do it right the first time. If you know you'll be doing a top swap in the future, do mods now that support those goals or just start buying the parts now, although to run the stock 3.8 you'll need a few mods anyway.
The intake is your choice, but I really like my Wizair. It seemed to produce great results and will work well for both a N/A and supercharged application.
Here's another option that many seem to like: http://www.grandprixforums.net/f73/4...take-2219.html
From there I'd jump straight to the S&S headers with a high flow cat while keeping the stock cat-back. You'll get a bit more volume from the exhaust while maintaining a stock-ish sound, just like you wanted. The stock exhaust is fairly small and will preserve that feeling of low end grunt, but won't be restrictive to you for quite awhile.
From there it's time to pick up a tuner and learn how to use it. You have more room for error without boost, so if you're going to try things out and learn the ropes, now is the time to do it.
With just those few mods you should be knocking on 14's if you have some good conditions and get a decent launch, and you won't have wasted any money on mods that you'll have to sell off once the blower is on the car.