Have you come across this car yet in your searches?
All new aftermarket ECU and harness setup using an LS1 throttle body on an Audi V8.
One of his for sale threads:
https://rennlist.com/forums/vehicle-marketplace/952320-boxster-s-race-car-with-audi-4-2-v8-engine-and-lots-of-motec.html
Thread here starting with a Suburu conversion, then ABZ V8. Most of the pics are gone in the Photobucket:
http://986forum.com/forums/boxster-general-discussions/25697-boxster-subaru-conversion-interest-13.htm
Much of what you are looking to do, but $10s of thousands invested. Sure that much of it can be done, scaled back, for a lot less. Sad there weren't more done like this one, no doubt that this one was sold at a loss considering the craftsmanship and hours put into it.
AND, don't forget about Vlad. I don't think he completed his swap, but lots of great info:
V8 Conversion
Rolling Shell - Follow My Porsche Boxster V8 Build
As far as S vs Base, from the transmission forward, I really don't see any difference in the mechanics of the swap.