Extremely Odd Electrical Issues - Car is Completely Dead

This is going to be a long one as it's got a lot of layers and I don't want to leave out any detail that may turn out to be important.

2006 Mustang GT, low boost single turbo setup, just dyno'd 500hp a few months ago. 40k miles on the car.

This started when I forgot to put my battery tender on the car after driving it and when I tried to start it the battery was completely dead. Pushed the car out of the garage so I had room to work, tried to charge the battery but it wouldn't take a charge. Odd thing I noticed is when the charger was connected there was a weird humming noise coming from the back of the car. At the time I thought it was from the rear speakers. It got louder with more amperage from the charger. Pulled the battery, put in another battery. Car fired right up and drove it around the block before pulling it in the garage. Put the battery tender back on it.

Now the problems start:
I try to start it a week later and the battery is completely dead (just a single click and nothing more). Remember the battery tender is connected. So I test the tender, it's working. I put a charger on the car and it takes a charge no problem. Wait for it to charge overnight. Try to start the car and I get a single click and everything goes dark (interior lights shut off, gauges shut off, etc.). Acts like a bad battery connection. Dig into that, find one battery connection a little loose, tighten it down, try again. Same thing, just a click and it all goes dead.

So I test the battery thinking it must be dead, it's got full voltage. Unhook battery, clean connections (even though they were clean), reconnect everything. Open the door and it's got power to the car again (lights come on inside). Turn the key and it starts making a weird clicking noise (relay noise) from the passenger side under the dash, gauge cluster is dimly flashing, and there is a hum from the rear of the car that matches the pattern of the relay clicking on/off.

So I turn off the ignition, get out of the car and notice the tail lights are dimly flashing at the same rate as the noise that's coming from the passenger side rear fender area. Try to lock the doors and they lock but then won't unlock. Use key to unlock door. Try to roll window up as it's halfway down from going down 1/4" every time I've opened the door. Windows won't work. Interior map lights won't turn on. Radio is dead, headlights are dead, gauge cluster is dead, power seats are dead, everything is dead other than the random relay and electrical noises. Unhook battery and all noises stop. Connect battery and noises return (no key in ignition). At one point a loud clicking noise under the hood turned out to be the throttle body fluttering.

Here is a video of it making noise as soon as I connect the battery. Tail lights are flashing at the same pulse rate as the hum you'll hear:

Throttle body fluttering. I don't even remember what combination of things I did before it started doing this as this was a month ago and it hasn't don't it since:

Here's what it does when I turn the key on/off, try to lock/unlock the doors, a quick look at the tail lights flashing, etc:

I tried to scan codes but since the car has no power (or intermittent power for only a split second at a time when the relay clicks) it won't connect to pull codes.

I tried pulling one fuse or relay at a time in the under hood fuse panel to see what would stop the noise. No relays changed anything when unplugged. Fuses 62 and 63 made the noise from the rear passenger side of the car stop when unplugged. Disconnecting fuses 46, 56, or 59 made new noises appear, always a rapid on/off noise from different components. No other fuses had any effect on anything.

At first I thought maybe the PATS stuff got triggered by all the dead battery problems but it's certainly more than that at this point (though I'm not ruling it out as one of many problems).

My best guess is that one of the many body modules somehow go screwed up and it's killing power to the rest of the car. Problem is, I don't know where all of these modules are, or how to test any of them as I don't have a dealer service manual for that sort of thing.

If anyone knows of a download link for the dealer service manual(s) for this car, I'd love to have it.

I've currently got a car I can't use, can't sell (for any decent value), and it's way too nice of a car to just rot away in the garage. It's already been like this for 3 months. I feel like this is the sort of thing that if I send it to the dealer (something I've never done in my entire life as I've always worked on my own cars), they'll spend a whole bunch of time (and my money) trying to figure it out and not ever figure it out since it's such a weird deal. Only chance at a dealer would be to find a really knowledgeable tech and that's difficult to come by.

I don't even know where to start with diagnosing this problem so I'm hoping someone has had something similar happen (though I doubt I'll be that lucky).

Any help would be greatly appreciated

Check for SJB water intrusion causes all kinds weird stuff and common issue. Specifically the Pats horn for the car alarm is in the trunk so sounds like that was humming from electrical noise from a short.

What is the battery voltage, measured at the battery, when it is making the clicking noises? Turn key to run, and turn on headlight switch when measuring voltage.

Service manual is available at http://iihs.net/fsm/?d=1. Have you tried a stethoscope or even a length of heater hose to locate the source of the noise?

I bet he has a dead battery. The noise is relays clicking in the SJB.

Testing a battery by checking voltage only, is not enough. Test it under load. Sounds like a dead battery to me too.

Ekis said:

Testing a battery by checking voltage only, is not enough. Test it under load. Sounds like a dead battery to me too.

Click to expand...

With key ON and headlamps ON battery IS loaded. If it cannot maintain 11.5 or better under those conditions, does a FULL load test really matter? Absolutely not.

JeremyH said:

Check for SJB water intrusion causes all kinds weird stuff and common issue. Specifically the Pats horn for the car alarm is in the trunk so sounds like that was humming from electrical noise from a short.

Click to expand...

The car hasn't seen rain in 4 years and hasn't been washed in a year (stored indoors). Anything is possible though so I'll look into it. Thanks.

Ekis said:

Testing a battery by checking voltage only, is not enough. Test it under load. Sounds like a dead battery to me too.

Click to expand...

Headlights won't come on but I'll do the test with the switch on and report back. The battery came out of a running/starting vehicle so the assumption was it's good. I'd feel pretty dumb if it's a battery issue but I'd also be relieved as I've not done a load test on the battery, just voltage test. There are those rare cases where voltage is good but it fails under load so thanks for that reminder.

Check voltage while the clicking is going on.

Remove the battery and put it on a good charger (12 amp or better). Then recommend removing, cleaning (wire brush) and reinstalling every ground connection in the engine bay. If you have an Volt/Ohm better check each cable/wire for resistance to ground and continuity from one end to the other. Additionally, find the grounds inside and in the rear of the car; there are a few under the dash; SJB and driver's side near the hood release and do the same thing. Floating grounds (grounds w/resistance) will do a number on these cars (ask me how I know). Suggest checking the fusible link; I've heard of cases where it's corroded internally but not failed completely setting up a high resistance condition. Once you verify all of the cabling appears to be proper then hook up a battery and start checking voltages. If you can get codes it might help point you in the right direction.

If you can remember the last electrical work of any kind you've done on the car I would check those connections as well. If still no joy let us know. I have a troubleshooting manual that I can copy out sections for you.

One other suggestion - in my own case my problem was a bad ground to the engine block which showed up as low voltage. I solved it by adding a cable from the passenger strut tower ground to a mounting bolt on the alternator. Problem solved.

Your case could be a short somewhere since you've found your battery dead twice. I would still recommend redoing all of the grounds as a first step. Note any corrosion you find and clean it well. I know some shy away from using dielectric grease but in some environments it works well. All depends on your conditions.

My guess is that there is a bad connection in the battery cables. Either at the battery, which is doubtful as it was mentioned that was checked, at the starter, or at the ground. A loose connection will act exactly as mentioned. Low amp stuff works, as soon as you crank it draws a large amperage load and will cut out if the connections aren't solid.

DieHarder said:

Remove the battery and put it on a good charger (12 amp or better). Then recommend removing, cleaning (wire brush) and reinstalling every ground connection in the engine bay. If you have an Volt/Ohm better check each cable/wire for resistance to ground and continuity from one end to the other. Additionally, find the grounds inside and in the rear of the car; there are a few under the dash; SJB and driver's side near the hood release and do the same thing. Floating grounds (grounds w/resistance) will do a number on these cars (ask me how I know). Suggest checking the fusible link; I've heard of cases where it's corroded internally but not failed completely setting up a high resistance condition. Once you verify all of the cabling appears to be proper then hook up a battery and start checking voltages. If you can get codes it might help point you in the right direction.

If you can remember the last electrical work of any kind you've done on the car I would check those connections as well. If still no joy let us know. I have a troubleshooting manual that I can copy out sections for you.

One other suggestion - in my own case my problem was a bad ground to the engine block whh showed up as low voltage. I solved it by adding a cable from the passenger strut tower ground to a mounting bolt on the alternator. Problem solved.

Your case could be a short somewhere since you've found your battery dead twice. I would still recommend redoing all of the grounds as a first step. Note any corrosion you find and clean it well. I know some shy away from using dielectric grease but in some environments it works well. All depends on your conditions.

Click to expand...

So you would do all that BEFORE measuring battery voltage while it is making the clicking noises? Why?

If you do all that, you have to wait hours for the battery to charge.....
If you measure voltage while its clicking, you have an answer immediately and know if its battery or a connection issue. OP also said he had a tender on it, AND already charged the battery. And it didn't help.

sounds like it could be the fuel pump humming. the fuel pump relay is not disengaging when the key is shut off. so its running or trying to run all the time, running the battery down.
It could be anything thats running with the key off. best option is to find the thing thats still running. put a descent ammeter between the positive cable and the positive battery post. you should see amperage bouncing with the clicking relay. find the relay and unplug it. That should tell you whats running. then you should be able to fix it.

Battery voltage should be measured about 24 hours after the last charge. A car battery is considered fully charged at 12.6 volts or higher. When the battery's voltage drops, even a small amount, it makes a big difference in its performance. Though not fully charged, a car battery is considered charged at 12.4 volts or higher. It is considered discharged at 12.39 volts or less. At ~11.5 volts the battery charge is around 10% of it´s full capacity.

Ekis said:

Battery voltage should be measured about 24 hours after the last charge. A car battery is considered fully charged at 12.6 volts or higher. When the battery's voltage drops, even a small amount, it makes a big difference in its performance. Though not fully charged, a car battery is considered charged at 12.4 volts or higher. It is considered discharged at 12.39 volts or less. At ~11.5 volts the battery charge is around 10% of it´s full capacity.

Click to expand...

11.5 is perfectly fine with key ON, engine OFF. You listed NO load voltages. A sulfated battery can read 12.6 without any load, and drop to way below 11 volts with a tiny load.

Mine shows 11.8 if I go to update my tune (flash) if the car has sat overnite. 12.1 max with Key ON ,engine OFF.

It can read perfect voltage and still be bad. It is not about voltage, it's about amperage. That is why they are rated by cold cranking amps (CCA). If a battery cannot produce the amperage or it can't flow because of connection issues you get no start. That is why you should load test a battery, not just measure voltage to determine if it is bad or not.

Last attempt here to make it as clear as possible:
If the battery reads good voltage at the terminals, with the key and lights on, a load test is irrelavent. There is an open circuit.

If there is no electrical issues with the car, a bad battery Will read low volts. Issue found.

In either case a load test is irrelavent, because a voltave reading gave me an instant answer as to what to do next.

OP stated he hears a clicking noise by the SJB. That means the battery has some charge. Measure the battery voltage and you have a direction to go about fixing the problem.

I cant make it any clearer.