I pulled the top console down and disconnected the 3 plugs. I turned the key and lights on and tested the plug that goes to the upfitter switches. There were 10 wires total. The only one that was hot was a purple wire with a grey stripe. Which I am guessing is the light for the switches, which has been working. The other are dead. Now I am about to ohm the wires from the plug to under the hood.
UPDATE: They are still not working. But I found out that the diagram that I posted in original post, Set A are the pass through wires that go to the passenger foot well. So set B must be the hot wires. I found that out after ohming them out. The manuel says it backwards. I still have no clue as to why they don't get hot. I couldn't find anything wrong in the top console with wires or plugins.