My point of concern though is do I have the right mix of control is Crypt > Null Rod. Artifact Mutation > naturalize. Drop magma jet for Rootmaze?
To answer your questions from my opinion. I personally believe that Null Rod is better then Tormod's Crypt in many situations. Null Rod is almost never a dead card, being dead in only most non-powered decks as 99% of people at proxy tournaments will run a few mox. Tormod's Crypt however can become very dead cards in such cases as Oath and other Welder decks can usually just play around it.
I think that you should leave Artifact Mutation maindecked and put Naturalize in the board. Not many decks besides Dragon or Oath rely on enchantments to win the game and theres are a numerous amount of decks however rely on artifacts for a win condition. Naturalize therefore I believe deserves spot in the sideboard so it can be sided in against those matches.
Root Maze is a very good card and should be tried to fit in as it is that good. However I don't think you should take out Magma Jet for it, Magma Jet provides you with something that you can't really find in Red or Green which is deck manipulation. The scry ability is the only reason it is the only 2 burn for 2 mana spell played in any red deck over something like Lightning Bolt.