2007 Ford Mustang GT, throttle body and communication issues.

My fiancé has a 2007 Mustang GT with about 31,000 miles on it. Recently it started having a long crank when it sat overnight, and it was cold. After the first start it would start fine the rest of the day. I tested the battery on Sunday with two different battery testers and it tested bad on both. The battery was a Duralast Gold that was six years old. We replaced the battery on Monday with a Motorcraft from the dealer since it was cheaper than the parts store ones. This is where the issue began.

After hooking the new battery up and going to start it, it started right up but it was idling kind of rough, and the rpms were only between 6-700 rpms with no high idle like it usually does initially. We have replaced the battery on this car two other times in the past with no issues.

I tried reving it up but it had no throttle response. I tried to drive it with the same results. The wrench light came on and then the CEL as well as a message in the display about a tire pressure problem which had never come on prior to this.

I put my scanner on it, and it has three throttle body codes in the PCM as well as some No communication codes in the ABS and IP modules. There was also a tire pressure sensor error in the GEM module. Throttle body codes are P2104, P2111, and P2112.

We have an Alldata subscription for the car, so I followed the flow chart for the P2112 code, and the test checked out good and said to replace the throttle body. I tried resetting the codes with the scanner, but they come back as soon as you turn on the key. I reset the KAM with the scanner with no changes. I tried draining the capacitors by unhooking the negative battery cable and then using a jumper wire to the positive cable with no results. This is also supposed to basically be an idle relearn since the scanner doesn't have the provisions to do that function.

I always remove the negative battery cable first when removing a battery and always put the positive one on first when installing it so I didn't ground anything out. All of these problems have come on with the battery replacement except the long crank time which is still happening. The scanner shows that the fuel pressure is fine as well as the car is getting a rpm signal, so I don't think it's a crank sensor issue and I'm not getting any codes for that circuit.

Has anyone had a battery replacement cause issues with modules or components? Has anyone had a throttle body go out with such low miles?

We are leaning towards replacing the throttle body with a Ford Motorcraft one, but the communication codes have me kind of worried that something else is going on since there are no comm lines going to the TPS sensor or throttle motor.  What else should I be looking at if anything?   Thanks.

I forgot to mention that the ABS and IC modules are on the high-speed CAN along with the PCM. I checked resistance at pins 6 & 14 on the DLC and I have 60 ohms so I know the wiring is intact.
The ABS com codes are: U1900-20 and U2011-20 which are a reception error and received invalid data. The ICM has the same U1900-20 code. To me this sounds like both of these modules are getting bad information from the PCM. I'm not sure if fixing the throttle body codes will resolve these too.

Hey Monte, hope you're having a good Thanksgiving.
I would try cleaning the throttle body if you haven't all ready.
If the ECM learned how to keep the engine running well with carbon built up in the throttle bore, the gets reset by disconnecting the battery, there's a good chance the engine will run as your describe.
As long as it's not a big chore, I usually just go ahead and clean customers throttle bodies during battery replacement without saying anything to avoid this kind of problem.
Hope that's all it is!

Thanks Noah, I hope you have a great Thanksgiving as well.
I did look at the throttle body and even though it was not really that dirty, I did clean it. I didn't take it off to clean it. Cleaning it did not make any difference.

We did order a new Motorcraft throttle body so we will see how it goes when it arrives.

This is the first time in all of the years that I have been working on cars that changing a battery has caused all of these problems. Doesn't make any sense to me.

Here is an update on the Mustang. A new Throttle body seems to have fixed the problem. Car now starts normally with no long crank and there is no wrench or CEL on the dash. I cleared the codes after replacing the TB and before I started it and none of the previous codes have come back. I just have a code for the monitors not being completed because of the battery replacement. Hopefully this new Motorcraft TB lasts longer than the original one. We took it for a test drive and everything seems normal.

Good news!
I have to believe it was a coincidence that the throttle body quit after battery replacement. Weird, but things like this happen. At least it was your car, that's hard to explain to a paying customer

Yes, it definitely had to be a coincidence, but I did find a TSB about codes P2111 and 2112 setting after disconnecting the battery and I think the long initial crank was probably throttle body related. Here is what part of the TSB said. "Some vehicles may exhibit diagnostic trouble codes (DTCs) P0505, P0506 and/or engine idle RPM fluctuation and hard starts. These vehicles may also exhibit DTCs P2111 and P2112 after KAM has been cleared, or the battery has been disconnected, or the vehicle had a dead battery. On vehicles with over 10,000 miles the issue may be caused by sludge buildup in the electronic throttle body (ETB) leading to airflow being less than desired."