Jim,
I don't know the difference between all the variants of the IO-360, parallel valve. But, you can read about it here if you haven't already.
For starters I do know a few things.
Get a forward facing sump for sure. You can bolt on a Superior or other brand cold air sump on just about any of the 360's. This will allow you to make a much tighter cowling. A rear facing sump is out of the question as your nose gear is directly behind the sump. (might fit with the long engine mount? I doubt it) But, I wouldn't let the "stock" configuration make me pass up a good deal on an
engine.
In my opinion, I would get a forward mounted prop governor. The back of the engine is busy enough I think, but I have the short engine mount..
Compression ratio will depend on what you want to accomplish. If you want to run MoGas for example, need to keep it rather low. 8.7:1 and lower I think?
It seems many of the other variants relate to what type of mag setup. I have dual impulse coupled Slick mags. But, this is 2013 now, and if I was starting over I would have some sort of electronic ignition on one or both sides. So again, the variant doesn't really matter as you would probably not use mags anyway.
So in summary, I would buy whatever is less expensive to get you the compression ratio you want, and the forward prop governor. Then, scrap the rest of it and
build it with modern aftermarket accessories. (Ignition, Cold air sump, Fuel servo, etc) So the actual "stock" variant isn't that important. Financially this may not make sense if your buying a new complete engine kit, rather than just the core parts. Maybe get some quotes from some of the build shops and only buy what you need, rather than paying for a sump and mags you don't want. Barrett comes to mind :)
Tom McNerney