2006 Mustang GT engine bog at WOT and briefly cruising

2006 Ford Mustang GT
U7140

I have finally decided after a long time of struggle with my car to come to the place where my answer may lay. I have been struggling with engine trouble codes thrown:

P0148= fuel delivery error
P0171/P0174= system too lean bank 1/2
P1000= OBD System Readiness not complete
P2195= O2 sensor signal (this may be caused from the cats not being in place)

I have a Predator tuner that is on the original tune as of yesterday, coming from a modified stock tune. I will be cruising along on my 63 mile one way commute on the interstate when I will get a slight area of rough running and flutter for a 5-10 second period then it returns back to normal, this usually comes when going up a overpass but that isn't always the case. Keep in mind my cruise is typically set around 75-80MPH. But I notice that 3/4 throttle it runs strong, but as soon as I go WOT, it starts bogging down and acts like I do not have the right air/fuel ratio (as if its too much gas or too much air dumping in past 3/4 throttle).

I am on stock tune and I am running 87 octane fuel. I have a cold air intake, a leak on the passenger side (bank 1) exhaust manifold (don't know if that effects anything), I also have no cats and magnaflow exhaust.

My guess of problem is (and I am no mechanic lol):
I think maybe this whole thing is just an air/fuel issue
The CAI on a stock tune causing mixture ratio issues
The leak in the passenger side exhaust manifold where it bolts to cylinder 4 (ordered replacement)

As far as the type of cold air intake, I wish I knew which one it was, I will post a picture to see if anyone knows which kind I have (bought the car used).

Help appreciated.