Car dies in idle?? Out of ideas?? Please help!!

Hello I have an 06 mustang GT. About a week ago the car started to sound weaker in idle and the battery icon came on. It would die on me at stoplights or in neutral (basically anything with low rpms). I replaced the battery with a brand new battery. Same issue occurred. I replaced the alternator, issue still occurred. I replaced the alternator connector because I noticed the clamp was broken, and the issue still occurs. I have made sure nothing stays on in the car and replaced the whole charging system. It will run as I am pressing the gas, but will die I'm mediately at low rmps. Maybe it's a short or blown fuse? Any ideas or tips would help. Thanks for reading.
 
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Hi, Sorry to hear. Did/Does your Battery drain completely overnight, Any CEL’s? Try turning off accessories while running, Stereo, etc. pull your Stereo Amp Fuse.
Did you see a “check charging system” on your display? It’s likely something simple, try these basic tests to check charging system, wiring integrity..
If it won’t idle, have someone hold it at 800-900 RPM’s with these tests, when required.

1) Follow the ground wires between the battery to the body and the ground wires from the body to the engine. Clean all the terminations and make sure the bolts are tight.
2) Follow the wires across the harness, look for any chafed Wires near sharp edges, etc.
3) Car idling, check your Alternator output Voltage post to it’s housing (ground) with a Voltmeter on DCV. Should be about 14 Volts.
4) Repeat the test, moving the ground lead to the Battery(-). Any drastic change in Voltage? Check Battery Voltage, Car idling.
There were a few TSB’s regarding rainwater infiltration ending up going through the Passenger side firewall, 05’-06’- causing mass corrosion, Grounding issues, issues with the (SJB). Another leak with the Coolant lines, same area. Just grab a light and take a quick peek up..
There was a recall for this, but they only ‘band-aided’ the issue.
5) The Alternator Plug is vulnerable to issues, I’d double check those connections, verify they're solid.
6) Car idling, Voltmeter on DCV, check the voltage between the negative battery post and the alternator Chassis & verify it’s zero.
7) Check your Positive Battery Terminal Wiring, Down to the Starter & larger wires to the Fuse blocks. Look for any wires melted on the exhaust, 02 Sensors, etc..
8) If you have no CEL’s, check with a Scantool regardless. Some Codes don’t present immediately, and you can watch charging system Voltage & 02 Sensors correcting, engine RPM, etc.
9) Check all your COP connections, Injector Plugs, etc.
These should give you a decent start.
Good luck! John
 
Could possibly be something in the ECU not allowing it to charge. Are you tuned? If so, you might plug in the tuner and see what the alternator readings are. I've seen the ECU fail in a lot of weird and different ways and the ECU controls the amount of current to all of the engine compartment as needed.

If the tuner (or scanner) reads correctly, then I would look at the BCM. These things are all great when they work, but they can be a pain to diagnose when something internally fails.