First thing you have to do is figure out your base defense, and at this point I believe the best option is to stay the course on converting to a 3-4, instead of reverting back to the 4-3.
While I've always preferred the 4-3, the 3-4 is more versatile on the field, and for the FO. It is simply easier to get the players to run the system, and they're typically cheaper than those required to run the 4-3.
If we run the 3-4 there will be quite a few skilled, young NTs available in the upcoming free agency market, and Brown is a beast in the draft if you go that direction.
My understanding was that the QB identified the Mike simply because he is the leader of the offense. He takes charge of most other things, so why not the Mike call too? Maybe the QB's better perspective of the defense because of a bit of extra distance between himself and the defense or because he's standing up makes him a better choice to make the call, rather than the center. Beyond that, I don't know if it really makes a difference who IDs the Mike.