Splashing black is interesting, but how is chains going to help you any more than root maze? Oath has intuition and impulse to dig for the oath if you have chains out, so it seems that the only advantage you have is shutting down their accumulated knowledge and recall. Is it worth it to kill your own draw ability?
I apologize, but I don't really see the point in comparing Root Maze and Chains. Half the problem with running all the mana denial, was if the opponent resolved a draw spell or two, they could undo a lot of the damage inflicted. That's why Chains is good, it shuts down Brainstorm, TFK, Standstill, AK, Ninja and Bargain preventing the opponent from recovering. The other thing I found was Bazaar was too slow; since it costed you much needed land drops and was subpar without running 4 Squee. So in addition to the speed issue, that takes up a lot of deck space since Bazaar isn't making mana.
You picked up factories and bayous? How does that help you at all?
Well black mana is kind of helpful when you run black cards.

Factories can be really any mana source, I just wanted a few more beaters in the deck. The important aspect of them wasn't the 2/2 beatings, it was that they could actually make mana. If BoB made mana, I might be inclined to add it even with the dis-synegry.
If you are going to run black, are you going to run deed at all? This thing has been my single most favorite thing to splash in tog or P/T funk since I got back in to magic two years ago. I see it missing from your list, is this because you felt you didn't need it? Or that it worked against you?
I had considered Deed and tried it. The problem stems from so much of your disruption being permenant based, that you usually set yourself back a great deal in exchange for only hitting 1-2 cards that matter. So Naturalize got the nod for the maindeck. It's a potential SB card, but I'm hard pressed to think of good times to use it with so many cheap threats in the deck.