2013 5.0 Gt O2/catalyst Emission Monitor Issues

I have researched this issue for days, and performed the Ford Drive Cycle a few times - I cannot get my Catalyst, O2, and O2 heater monitors to go to the Ready state. I got the car used, so I am not 100% sure what had been done to it, but I know bolt-on mods are on it. It has a K&N cold air system and box, and Flowmaster after axle mufflers. The rest of the exhaust is stock and the cats/O2 sensors are there. Not sure if there is a tune on it, but doubt it. I can see the downstream O2 sensor voltage on my bluetooth OBDii reader and Torque app, but no upstream O2 sensors (due to it being wideband and Torque does not register this). I have put almost 1,000 miles in stop and go as well as open highway driving (staying under 60 mph as the drive cycles require).

The car sit for several months, and when I tried to start it the instrument panel wigged out due to a very low battery that went bad. Not sure if that hurt anything(?) I replaced the battery, but cannot get the damn thing inspected or registered because the last three monitors have shown incomplete for weeks. I am not sure if I need to reset the PCM again by pulling the battery cables and discharging as i would SURE hate to spend weeks again just finding out that did not help. Does the PCM stop trying to perform these tests after a certain period or number of tries requiring a reset?

Any other ideas?

Took your advice JKidd and took it back to the dealer to ensure the stock tune was in place. He did ask when I dropped it off if it had a tune and I told him "I" did not put a tune on it, but it was a certified pre-owned vehicle we purchased from them about a year ago and I "assumed" they verified the stock tune was in place... I got a call the next day saying it is ready to pick up. I asked what they did and was told "the tech just drove it for 10 minutes and all monitors changed to ready". I told the service adviser right then that did not sound right as I have driven the drive cycles for over a month and about 1k miles.

I picked up the car and checked the monitors with my OBD scanner - sure enough, they were all ready. Started to take off and it was all I could do to feather the clutch to keep it from bucking. Hmmmm. Got on the highway and it felt like I was towing a 10k lb. trailer behind me (low on power), also at a steady RPM I could feel the engine surging constantly. Coming up on a car I lifted my foot from the accelerator pedal expecting it to engine brake and slow down as normal, and the RPMs stayed high like the accelerator pedal was stuck - I almost hit the back of the car before I hit my brakes. At my exit at a stop light, the idle was hunting all around and almost died on me on one stumble. Something was not right. It almost feels like I need to run an idle and PCM relearn(?)

I called the dealer back this morning and told the service adviser about the changes, and I was pretty sure the PCM had been reflashed. I told him I did not care, but as the owner I needed to know this info, and if he would please go back and talk to the tech and verify. No return call...

Anyway, I 'think" my used GT had an aftermarket tune and that is why the monitors would not ready. Sucks too, because the "old" GT ran a hell of a lot better than what I an seeing now! But, at least it is inspected now.