James - excellent write up of the diagnosis .Thank you for sharing.So often such Threads just die or the OP says "it was 'the' relay".
So your problem was 'just' the faulty SAI pump motor relay ? Part #: 993-615-115-01
http://www.pelicanparts.com/catalog/SuperCat/986M/POR_986M_FULEMI_pg3.htm
No vacuum leaks, no vacuum component failures?
I ask because one of the causes of relay failure is a defective SAI pump that draws too much current because the bearings are worn or it is literally falling apart inside the case.. The pump can be rebuilt but it is tedious. More in Search.
http://rennlist.com/forums/996-forum/735878-sai-repair-diy.html
How did the SAI pump work with a faulty relay ? Because you hot wired it ?
btw ,if that relay is like mine, it is an oddball pin orientation - in case others think a generic will work.
Considering the frequency with which this subject comes up, your diagnosis will be very helpful to other Forum members.
It certainly makes the ROW reflash seem appealing -if that is still available?
ECU Doctors used to offer it for $500.
http://www.ecudoctors.com/porsche-boxster-ecu-performance-tuning-flash-2.html