What Michael said. I've done some 'matched pair' experiments, and it's not all that easy to control everything you must to get them to sound 'identical', even using 'the same' wood for both guitars.
Guitars are really complicated beasts: that's what makes them interesting, both to build and to listen to. It also makes them hard to sort out. That's one reason we get into the long discussions here over seemingly simple questions: there really are no simple questions in this business.
Another thing that contributes to contention is that we tend to use terms differently, and particularly if we come at building from different directions. If you ask some question of a 'traditionalist' and a 'technoid' you're likely to find them breaking chairs over each other's heads in fairly short order. The funny thing is that if you presented them both with the same three guitars and asked them to rate them they'd probably agree, and if you could translate the terms they use into the other guy's language you'd find they were saying the same things.
Traditional or techie, you're either going to have to build a number of guitars before you can start to sort it out, or else you're going to have to find somebody else who has and is willing to tell you what they've learned in a way you can understand. Since I have no idea which approach you find more comprehensible, I can't tell you how to proceed.
This is not to say you won't learn anything from either of the experiments you've proposed. Just don't be surprised if what you learn turns out later to be wrong, owing to some other thing that you didn't know enough to look at, at the time. It's all grist for the mill.
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