I'm doing the same thing as you, and picked a Boxster S as what I consider a semi-kit car. I'm now taking old lower performance parts off and upgrading - so far it's been fun and rewarding as I have a car i can tweak a little at a time and keep making faster.
I faced the same decision as you about a year ago, and decided the 986 was the way to go. When I bought, the 986 prices in the southeast were much lower than 987 prices, leaving more for modifications, so that's the way I went. The suspension geometry, etc. is all the same, so I believe there there is very little difference in performance potential.
Either way, you can't go wrong - good luck.
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Kippis

986S
991S
Van Diemen RF97
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