I assume the CPS3 works fine on the 5.1 board - the v6 doesn't seem worth the increased price to me, unless there's a reason I should be going for the v6?
All I know is the 5.1 board does not play well with power supplies that have a 3.3v rail. Every cabinet I tried it on that had this, it would fail to boot. So as long as you aint using one of those, 5.1 should work just fine.
One of my cabs has a 3.3v rail, the other doesn't.
I do have a CD drive though so I can use that if I put it into that cab. The SCSI2SD is more if I'm using it on a Supergun it's a hell of a lot less of a pain to move it around