Did Porsche set the rear wheels too far forward?
 

Today I was pulling my CV joints in preparation for gearbox removal, and noticed that the half shafts angle quite a bit in the fore-aft direction. It looks like if the rear wheels were set about 50 - 60 mm further back, they would line up much better, and then the CV joint wouldn't have to do quite as much "angular work".

I've always heard the Boxster S is hard on CV joints - perhaps this is why. I wonder if there is this much offset in the base model transmission, or the automatic?

Nope. It's perfect the way it is. ;)

perfect or not, with the introduction of the 's' model in 2000 they added the 6-speed without changing most other aspects of the suspension/chassis geometry. the 6-speed is longer than the 5-speed transmission, hence the greater offset on the drive shafts and resultant increased cv boot wear.

Thanks for confirming my suspicion about the transmission vs. wheel placement.

The 6-speed was made for the 996 & adapted to fit in the Boxster S