I don't run rears, never have. But you do need front ones and if they aren't good it will cause you all sorts or problem.
The tuner does need to turn off the rears if you're not using them or you will get CEL like chris said.
Alright Just got back from the tuner. Previous owner mover the front o2 sensors to the bottom side of the headers so they were hard to see. I had him make sure they were turned off and he made some adjustments to the tunes. After 2 more burns its running almost perfect. Even feels like it picked up a little more torque. He admitted to me that he was using a premade split port file with small adjustments and he is now going to make me a full custom tune. He also told me he would give me $50 off on the dyno run so I'm going to dyno tune it and post some numbers (even though they won't be as impressive as Orange's)