check engine and AT lights activate upon flooring the accelerator pedal

Hello, my name is Daniel and I'm working on a 2005 Mazda 3 2.3L replacing the MAF sensor and the neutral switch. Prior to this service, the car has been rough idling since it was purchased three weeks ago and the data pointed towards the MAF and a no start in park points to the neutral switch. Once the parts where replaced the car went into an operating mode I've never seen before. When the car is in gear and moving I can't floor the pedal without causing the AT and Check Engine lights to come on and causing the car to behave erratically, even shutting down cylinders 3 and 4 until I turn the car off and start it again. Once restarted the fault lights remain on and the accelerator pedal won't respond for the first 2/3 of the way down, making the car not accelerate past 3k RPMs and the no WOT. I've cleaned the fuel injectors and lines, Baro, MAP, MAF sensors, Purge Valve, throttle body, replaced bank 1 oxygen sensor 1, spark plugs(used OEMs), transmission oil and filter change, engine oil and filter change. Did the idle relearn procedure and nothing happened to change problem. Help please!!!!

Hey Dainel! Do you know what the trouble codes are, or have access to a scanner? That'd be the place to start. Even taking it to (insert parts store brand here) and asking them to scan codes for you would be helpful.

If I had to guess, I'd suspect something wrong with your new MAF, or the wiring to it. If you have a multimeter and some T-pins, I can suggest some quick wiring checks at the MAF.

Thank you so much for answering so fast, I'm lost on this one. I'm going to try to upload some images of codes and a Freeze Frame.

I can't seem to be able to upload the images. Here's the list of codes:

P2229--BARO Sensor Circuit High Input

P2138--Throttle Position Sensor

P2122-- Throttle Position Sensor

P0113-- Intake Air Temperature Circuit High Input

Here's the Freeze Frame

The wiring harness looks good without cracks or brakes, the multimeter reads continuity. The scanner live data reads the MAF fine but can there be a connection failure somewhere away from the plug harness itself?

Ok, cleaned all body connected grounds, went and cleaned all the sensors and harnesses again, cleaned the throttle body as well just in case. Nothing... Cleared codes and the P2138 was the only one that came back. Here's the data from that code. I'm so grateful for your time, I'm in Puerto Rico and I find it hard to find data analysis in my area. THANK YOU!!

Freeze Frame #2

BTW, I'm almost sure that data came during the test run as soon as I floored the pedal and the fault code activated. This wasn't at idle with the car parked.

Does your scan tool have live data to view the app voltages? If not this can be done with a multimeter as well.Tyler will be able to guide you through these tests (not trying to step on any toes buddy) it's just funny I just dealt with a jeep this week with an app problem a lot like this and the problem was not getting a full 5v on the 5v ref line causing to much of a difference at wide open throttle

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Hello Ben, thanks for the input, here's what I have.

This live read is with Key on-Car off pedal at top. This next read is with the pedal all the way down.

This capture is with the car on and pedal all the way down.

If that data is accurate, then it appears that both potentiometers in the APP sensor are barely moving.

Try observing your scan data again, but while slowly sweeping the pedal all the way down and all the way up. There should be SOME kind of change.

Key on, backprobed at the APP, you should see the following values:

Green/yellow: B+
Grey: Either the .85V or the 3.3V reading you saw on the scanner.
White: Same as above
Gray/yellow: 5V
Yellow: 0V
Black: 0V

Thanks, as soon as I get back home I'll run the data to checkout the numbers you gave me. In the meantime, I was going through the service manual and it mentioned that I should not have continuity between the terminal C on the MAF/IAT harness and a body ground, but have it from PCM 1AK (harness side) and terminal C on the MAF/IAT harness. I made the test and had continuity from the body ground to terminal C on the MAF/IAT harness. The solution offered was to replace the harness, which I did and still nothing changed. Before making the change of the MAF/IAT harness, I tried a little resetting trick I learned at my father's shop. Since the car won't go past 3,000 RPMs at supposedly WOT, I floored it and while it revved up to its limit of 3,000 RPMs I rapidly switched the ignition switch off and back on again for a split second without letting the engine shut off, at the moment the switch goes back to the on position and the engine catches again, release the accelerator pedal. This process for some reason resets something, the AT light goes off and the throttle responds to the accelerator pedal signal to the point where I can drive the car granny style without flooring it or trying to engage the overdrive, because doing that brings back the cylinder shut down issue and the original problem. The throttle response after the reset doesn't completely gets fixed, if I rev it slowly it'll get to about 4,500 RPMs before the problem returning. After the reset the minimum touch of the accelerator pedal generates a response at the TB even though it refuses to go on WOT. I'm even more confused now.

Since I've seen that it was the timing that caused someone else the same problem, I checked the timing and the car is properly set in time. That rules timing out.

I'm sorry, I mistakenly said in my introduction post that the cylinders that shut down were 3 and 4, it really is cylinders 1 and 2 that stop working. Sorry for that, just noticed it.

Did you do the tests Tyler suggested? That's where your problem is.

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Hi there Ben. Yes, I did the test at the APP. I actually went further, I found another pedal from a 2011 and measured that one as well, there's no difference in pedals that I can see but maybe its different. I'll post pictures. This are my readouts:

At the harness:

Green/Yellow= B+
White= 11.7v
Black= 0.0v
Yellow= 5.0v
Grey= 0.0v
Green/Grey= 5.0v

At the APP (oem pedal):

Green/Yellow= B+
White= 1.1v
Black= 0.0v
Yellow= 5.0v
Grey= 0.0v
Green/Grey= 5.0v

At the APP (Extra Pedal):

Green/Yellow=
White= 1.0v
Black= 0.0v
Yellow= 5.0v
Green/Grey= 5.0v

After clearing codes and restarting the car, the problem went away for a couple minutes and the signal disparity spiked again. Could it be the PCM or Throttle Body Sensor? Don't know if the bad signal creating the issue is bad coming from the PCM or throttle body sensor. Either way, the numbers I got differ from Tyler's. Don't know where else to go here, very frustrated.

*OEM 2005 Pedal = Ending in -AH
*OEM 2011 Pedal = Ending in -AK