Limp home mode and odd code P061

The codes P201 - P208 are not valid codes. Codes must be 5 digit with the first digit being a letter as the other codes you listed were. It sounds as if you have more than one concern present. The concern you've had for like 6 months now with the P061B and P2106 is most likely related to the throttle body/TP sensor assy. Buy a new throttle body assy, not a used one, and replace it. Clear the computer memory and go from there. Drive it awhile and see if any of the other codes return. The P151a is related to a intake manifold runner control actuator concern, and the P0446 as you already know is related to the evaporative emissions system. I wouldn't worry about those unless they return.
 
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The p201-208 are p0201 and are a failure detected in each injector (hence the 01-08). I've looked up all the codes and know the causes and I have replaced this TB and TPS with a new 07 revision one and the problem still persists. This afternoon, the car will have all the PCM files reflashed/updated. A mechanic I talked to thinks that the problem could be with the PCM files as it is a known and common problem on 05-06 Mustangs. I have not taken the car to a dealership as it is out of warranty and far cheaper for me to replace the few parts that have been done so far. I have also not had any recall notices sent to me so the normal time Ford updates the PCM have not occurred for this car. I will disconnect the battery after the updates as it seems that causes a failsafe within 24 hours.

It is entirely possible that the original TB and TPS went bad and when I replaced it with the new style and no new calibration, the systems parameters are still off.

As for the injector and CMCV codes, I will wait to see if they come back. I am afraid the EVAP purge solenoid will need to be replace but that doesn't seem to be causing any issues other than the possible start up here and there.

I will report back what I find out.
 
If it were me and I was certain the throttle body (the most common cause for these codes) was not the concern of the P061B and P2106 codes, I would stress test the ignition coils and replace any that fail. Stress testing the coils requires an oscilloscope so it may be hard for you to find someone other than a dealership to do this for you. You could of course replace all the coils, but that isn't very cheap. When ignition coils begin to fail they will cause excessive radio frequency interference (RFI) which reeks havoc with the PCM and can cause the problem you are having. Having worked on lots of Mustangs, this would not be my first inclination as the cause of your concern, however I have seen it on many Lincoln LS's.
 
I wonder which would be cheaper, going to a dealership and having them test them or just buying new ones... The PCM updates are only $45 so I will start there since I know I've never had it done. Thanks for the heads up on the coils.
 
Have you checked with your tuner? I would throw the p061 code at anything above 1/2 throttle when cold. He fixed it as soon as I told him what was going on. I also sent data logs of the problem replicated.
 
As I mentioned on the first page, my car is stock. That means stock tune as well.

My codes seem to actually be caused y a non-OEM drop in filter. (unknown disposable brand). Foam was too think and the box wasn't sealing all the way and allowed particulate in to the MAF. Happened at the end of WOT runs because it was sucking the hardest at that point. Also happened in the rain because of road spray. Ordered and received a WMS High Velocity Intake. Will install soon and see if my problem is solved.