You say identical down to the neck blanks and such, but mention topwoods being different, so I assume you're only talking about the body slab and neck sans-fingerboard... and all else can be variable.
Were you literally considering somehow making it such that you could redo the boards and topwoods somehow? otherwise, if one or both are really irreversible, as I figure they are, then you'd have to pick between keeping mech/elex the same and comparing woods (and picking one to change top OR board) vs keeping ALL the woods the same and comparing mech/elex (which of course can be done a buncha times with multiple different things).
There was a huge J pickup shootout years ago where they made it real easy to swap pickups on the fly, you might consider that kinda' thing if you wanted to do preamps/pickups and such.
Comparing bridges definitely a good idea... punch vs compression/sustain is usually mentioned on either aluminum or steel vs brass (respectively). Cool to kinda' verify it quantitatively somehow.
You could also compare strings, but then you'd want to come up with something in the jig to hit the strings identically each time and on both instruments.
Comparing topwoods, boards, nuts, frets, etc, would all be really cool, but the nature of how one might change (or even make it possible to change) those might negate the consistency/reliability needed for useful results.
One variable at a time. That's the rule.
Just some general thoughts.
