Sounds good.
I can give two pieces of advice for personal experiments/mistakes.
My first experience, which was not a mistake, was to rotate the air filter housing 90degrees, as you have mentioned. I couldn't detect any noticeable change. Now, granted, I didn't go to lengths that you will in opening the filter mouth.
As for the muffler drill, I would consider this a good idea. It should open up some deep tone without affecting bike function. And, as you said, it's reversible.
I will warn you against drilling or punching the baffle that is down inside the muffler. I, on a curious afternoon filled with stupidity, decided to drive a punch down into my muffler and open up a louder exhaust note.
THIS WAS A $600 MISTAKE. It makes the muffler sound like....well it made it sound like it had a hole in it. I was so obnoxious that I shelled out the extra cash for replacement muffler.
Bottom line: If you get a whim of curiosity and decide to try it out.....
DON'T.
Let us know how your experiment goes.
-Jonathan