Well you're going to have a couple of other challenges where wiring is concerned. #1, you're going to have replace the OBC, which i'm assuming you got with the new engine yes? I'm not 100% positive on this or not, but the instrument gauge cluster you have in your car, and that of the cluster found in a boxster S are 2 different versions... I believe it's similar to people who have wanted to swap in the 996 cluster in their boxsters, but I'm not 100% positive. That may be something you need to research more. The new 3.2 L OBC will be configured to a 3.2L's specs. However, because you have bored the engine, you will likely need to find an indy shop capable of "tuning" the engine. The MAF may need to be re-mapped among other things to fully take advantage of the performance specs.
The A/C controls (HVAC) control unit should be plug and play, I don't see there being anything different between these modules.
If the car has not been equpped with the "third radiator" already... you'll definately also want to make sure that gets installed as well. The 3.2S comes stock with 3 radiators, with the third in the middle. Has the car already been fitted with a Boxster S front bumper? Not sure if it's 100% necessary to put the S bumper on, however, that particular bumper has an air opening for cooling of the third radiator. Obviously the lines also have to be run to this radiator.
While we're at it, we might as well discuss the brakes and suspension. The S uses bigger rotors (cross-drilled) on both the fronts and rears, as well as larger calipers and pads among other things. It "may" be easier to purchase the "BREMBO" big brake kit, rather than trying to find Boxster S parts for all of it. You'll get the same if not better performance out of them, and it may cost less in the long run than having to hunt down all the parts. Just my thoughts there.
The suspension... the rear and front sway bars are more robust than a standard boxster, along with the linkage. These can be swapped out, and should help with overall stability. Since neither the S or the standard boxster were really designed for a larger engine like the 3.4 (at least on your year and model you're working on), and considering you're specing the car out for race... I would also suggest a more heavy duty engine mount. There are articles on how to swap in the 996 engine mount, which i believe would suit your purpose. There are some aftermarket ones that are out there, however, I have heard bad reviews on them and them causing more problems rather than fixing them.
As for the ABS, I'm not entirely sure as to the differences, someone else would need to chime in to give you some sound advice there.
One other thing you really should consider... again, with the intent of "racing" in mind. Replace the factory 3.2S AOS (Air Oil Separator) that's on the engine with larger more robust MotorSports AOS. It's a 2 compartmental true AOS as opossed to the factory ones that come on both the non-S and S engines, and it's meant for higher G-Forces (especially on cornering). Last time I checked, Sunset Imports can get the MotorSports AOS (which is a special Porsche order item) for $150, which isn't too bad all things considered.
Hope this helps. cheers