Mike, very nice work on your case. Is Olies just a machine shop or do they provide other services?
Kevin, I found this vid on YouTube. It looks like they have a jig. They probably indicate off both the bores as well as the transmission mating flange. Looks like the case has through bolts and perimeter bolts installed, although no way to tell if it has or hasn't already been shuffle pinned. Boring starts at the 35 second mark.
Porsche 911 Machine Work & Racing - YouTube
I have a decent idea about how they would go about doing the boring job, but I have a harder time figuring out a good way to do the shuffle pin machining. I mean you've got to be dead on, you're working with two separate pieces, and trying to get them to match perfectly. If I have this done to my case, I would definitely be taking video or at least pictures.