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Hello fellow Mustang bloggers, this is my first time posting in a forum, I usually do not post anything because I mostly just come here to find help about problems that are not that complicated however today something crazy happened that has me scratching my head in confusion. To begin my story let me know what I had been dealing with before this crazy incident. My 2006 Ford Mustang GT 4.6L 5speed manuel was purchased almost 4 months ago. @ 55k miles. occasional PO340 or PO344 trouble code. seems to stay away when the weather is dry. buy very random otherwise. car runs fine swapped positions sensor same code comes up on the same passenger side bank.

Today during my 20 minute drive my mustangs abs, the light the comes on when your loosing traction. and the off light on the traction control all come on at once. (ok maybe small glitch or i really did loose traction carried on) continueing to drive the not wearing seat belt lights come on, then they all turn off. then the light that turns on in the dash when you pull out the key turns on blinks a couple times then turns off. then all the other lights turn on and off. (ok cool something really wierd is going on (thinking pcm problem maybe, or short of some sort). Next aftermarket sony stereo screen turns off randomly. Next windows do not roll down. after parking the car, I think maybe shutting down and starting up again? Turned car off. Then car didnt want to start, cranked a little then just a bunch of click click click. Ok so then I get a jump from a big truck let the battery charge a bit from the trucks alternator just in case. drive car home. and replace alternator. after replacing the alternator I notice the car idles a lot smoother, however lower 5-6k somtimes down to 4 occasionaly. ok cool not a big deal. however aftermarket stereo screen wont come on. The buttons are lit up, it connects to my phone but no screen. Also now the passenger side auto up does not go up automatically. and after turning off the car closing the door, and locking it I realize the buttons from the aftermarket stareo are not turning off (never did this before). Yes I unplugged the battery while I replaced the alternator. checked all the fuses everything good there. Please help, any ideas are greatly appreciated!



2006 Ford Mustang GT
1998 GMC Sonoma SLS
2014 Kawasaki Ninja ZX3R
 

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This might sound silly, but my friend did do this....Did you confirm that you hooked up the alternator correctly? My friend installed his reversed....so it would take electricity rather than making it. Caused all sorts of random electrical problems. Being that you are having some problems here, then there, then over there...etc.

This was an old pickup....but the symptoms are the same...and it may not even be possible to mess it up with a mustang??? So keep that in mind....Just trying to help.
 

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I think all the weirdness with the flashing lights, etc. happens when the battery is on the edge of going dead; and also can happen when the battery is not fully charged or has just been replaced. My car did some similar things and and haven't really figured out for sure what was going on, but it was battery related.

Make sure the battery is fully charged -- either put it on a good charger or drive around for a while. See if it goes away . . . or, you might have a drain on the battery; I seem to have one but haven't solved it yet.
 

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If the problems happen mostly during wet weather, then water dripping onto the SJB (smart junction box) may be the cause. It's located behind the plastic kick panel in the passenger side foot well. If the carpet is wet or damp in that area, then look for water leaking into the interior above the SJB.
 

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The passenger side auto up most likely needs to be reprogrammed. I believe just roll window all the way then down manually does it but check the owners manual, Mine has done that a couple times when batter died.
 

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You have an 06 and didn't say the age of the battery. I find they last about 5-7 years so if this is an original battery, time to change it regardless of mileage. The clicking noise you describe sounds like your battery is toast too. And the lower idle suggests your alternator is trying hard to charge the battery and loading the engine. New batteries are less than $100 at Costco. Try that next.
 
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