nlerner had a Kogswell PR2 at some point, but sold it. He'd be able to give you the complete lowdown on this frameset.
Firstly, I would suggest bringing the frameset to an LBS that has the experience and proper tools for checking out frame alignments. I had heard that the PR2s had some serious production issues, leading to frames that were shipped with bad alignments and frames that wouldn't track straight when built up. Since you got this frameset for a song, I'd spend a little money and have all that thoroughly checked out before you put a lot of money into it. If it checks out, then you've got a really nice 650B frameset to build up!
I like your proposed build list, but if you're going to go with a 9-speed cassette, I'd consider going with modern shifters, and possibly indexed. I'm running an 8-speed cassette with a vintage derailleur and Suntour bar-cons, and I find that tiny movement of the shifter can result in chatter or ghost shifting. These shifters were designed for much narrower 5- and 6-speed freewheels with wide spacing between the cogs.
For wheels, I have the 650B Synergies and they're great. I bought them from Anthony King/Longleaf Bicycles and had him build them up around an Ultegra rear and Shimano dynamo hub front. I'm running 42mm Hetres on them and love them!
From what I've read, the Pari-motos are wonderful riding, fast road tires, but have very little tread depth, and wear out very rapidly. They're made more for single, long events like PBP, then get thrown away. The Hetres should last a lot longer, can be used on gravel and dirt trails, and since the PR2 frame can fit them just fine, why not?
By the way, here's my 650B wheelset on a frame that I converted from 27" to 650B:
