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S or non-S isn't really a big deal. Certain years make things a little easier, electronically, but other than that its the same chassis. Swapping the gearbox isn't a big deal, as for brakes the factory S brakes are plenty- heck, unless you're on the track the base Boxster brakes are plenty with good pads.
As to which years make the swap the easiest, an 03-04 car is perfect, as you already have Motronic 7.8 which is plug and play with a 3.6, and not very difficult for a 3.8 if you went that route. An 00-02 has Motronic 7.2 which is a relatively simple wiring harness mod to run connect to the 7.8 DME you'll need for the 3.6. A 97-99 car has Motronic 5.2 and requires a bit more harness work to interface with the newer DME and you'll also have to install all of the E-Gas guts.
The person to ask regarding all of this is Tholyoak.
Just a question, but why not keep your current S and just swap the motor?
Patrick
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