I find myself always returning to a chess analogy in questions like this. Yes, there are specific strategies and formulas (I use that term loosely) that can help in controlling and shaping the tone of an instrument, but they would take far more than a few forum posts, or even a single book for that matter, to teach in any depth.
Like chess, learning these strategies can be done to some extent in abstract study but you do not gain the same understanding as you will by playing. Tutelage and guidance can certainly speed your improvement, but you still have to do it to learn. And judging the wood in your hands is every bit as complicated as judging the player across the board from you. Perhaps a hard formula would be possible to predict outcome and determine strategies, but it would require so many variables that it would take a Big Blue to run it, and a team of engineers and programmers to measure and enter them for each piece of wood.
People like Alan are an excellent resource to have around, to at least offer some well thought out general and specific advice, backed up by a wealth of experience. Even then of course, descriptions of tone are still so metaphorical and subjective that his "punch" and "bass" may not perfectly match the definitions in timbre that you've applied to them in your own mind. You're on the right path to be thinking of these things and asking these questions, but of course it will still take your own experimentation and listening to bring a tangible understanding.
I think this same analogy applies well to everything from tap tuning to setups. The best advice I could offer is to tap and flex every piece of wood you pick up along every stage of the building process. A few guitars and you'll begin to think you understand what's going on. A few dozen guitars and you'll think again that you don't. After that you'll hopefully start to find a more regular increase in consistency with your intentions and expectations.