[78F350]

There's plenty of reading you can do about S vs base with a simple search. Both can be good cars, I don't see that or the mileage you posted as being the most important issue - You already said that you are fine with the '99 vs S.

More important is how the car has been driven and cared for. If you are buying from an individual you can usually tell if they have cared for their car.
I have a 99 that still smells like fine leather inside and most of the trim pieces look new. Engine and suspension clean and no signs of deferred maintenance. (I bought it with about 80K miles from a salvage auction with minor collision damage.)
I also have a 2000 S that smelled like an ashtray inside, broken trim, mis-matched tires, and a long list of jury-rigged repairs.
Get the idea? A Boxster with 200K miles that has been cared for by an enthusiast can be a good car for another 100K miles. One with 50K miles and a history of neglect can cost more than the purchase price to get another 1000 miles.

Edit: and regarding the year/IMS, I have pulled apart two 2001 engines and both had an original dual row bearing. If worrying about the IMS is going to detract from your enjoyment, buy a car that has a verifiable replacement, or have it in your budget to have it done.