I went through the same analysis
I don't have the link to 'my' thread handy, but I posted the same question long ago, got a ton of thoughtful responses, and ultimately purchased a low miles 2003 S.
I saw the exact same Consumer Reports, however, if you'll look at the 2007 cars edition, you'll see they said don't buy a 2004, and 2003 was great, and they don't explain the total reversal, so I lost faith in that measure.
I found a comprehensive aftermarket warranty for 5 years for under $2k (not a ton of mileage allowance, but that's fine for me).
I prefer the looks of the 986, and felt I got more for my money.
It is ultimately a personal choice, but I have no regrets having gone for the "S".
Good luck in your search, and please keep us informed.
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2003 Boxster S - Speed Yellow
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