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I have a 1999 dodge dakota with a 3.9 v6 magnum. The motor was replaced with a rebuilt one and it is sound and tight. However, the truck will cut off and not start until what seems to be after it cools down some. Then it cranks runs perfectly for awhile and then again shuts down. There is a lot of excess heat under the hood but the truck is not running hot. I have installed a new crank position sensor, tps, iac, temp sensor, etc. Point is nothing stops the problem. Once it cools down it runs perfect until it gets to a normal operating temperature and repeats the problem. Anyone have a clue to what this issue is?
 

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There have been a few threads posted by people who have had sort of kind of the same intermittent shutdown issues (I can't remember how many of them have been shut downs with engine warm) and some of these people have actually followed up (which is way rare around here) & some of these people have reported that it turned out to be the PCM.

My own PCM had to be repaired a few years ago, but the intermittent shut downs were totally random & not related to heat.

You can troubleshoot this when the engine is in the crank-but-will-not start-mode. Basically you are looking for battery voltage at the coil within 2 seconds of turning the key on (which would indicate your ASD relay is good) and then you are looking for a trigger signal, with a test light, FROM the PCM TO the coil. No trigger signal would indicate that:
1)the cam position sensor (aka distributor pickup coil) is bad
or
2)the crankshaft position sensor is bad
or
3)some where there is a glitch in either of the above circuits to/from PCM
or
4)if all that tests good, the Haynes (yes, the much maligned Haynes) says to send the PCM out for diagnosis & repair.

That was the troubleshooting sequence that I used to narrow it down to my PCM.

Somewhere on this site I have spelled out this troubleshooting sequence; I'll see if I can find it somewhere & copy & paste it & if you want you can try it when your dak is in the no-start mode.
 

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Okay, here you are:


post #9 covers that piece of troubleshooting I just alluded to.
You might want to read through the whole thread, you may find it applicable to yours; his was rather similar & it did turn out to be a loose pin in his PCM.

As far as the troubleshooting, my Haynes is for '00 through '04 and I don't know if the wire colors are the same. I now have a FSM, but it is specifically for an '03. However, give me a bit, as I just remembered I do have a Haynes that covers '99 Daks; I'll take a look in it in a bit & see what color it claims the wires should be.
 

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My '97-'99 Dak Haynes says that the coil driver wire is black/gray and voltage is dark green/orange.

(However, the caveat is that this is from a Haynes.)

But first, when it is in the crank-but-will-not-start-mode,
do you hear the fuel pump power up when you turn the key from off to on? If you have a fuel pressure gauge (relatively affordable) you could hook that up to the shraeder valve on the fuel rail & see if you get fuel pressure when you crank, even though it's not starting.

When it is in the crank-but-will-not-start-mode,
if you have fuel pressure at the rail, it is always possible that your injectors are, for some reason, intermittently in a mode where they aren't pulsing and your engine is not starting. That can be checked as well, but if you have fuel pressure at the rail, then I'd check for spark. I'd check that there was voltage from the coil to the cap first. If there is, then I'd check to see if it was getting through the distributor cap to the plugs. If no voltage from coil to cap, then I'd verify the coil was good. If it is, then this is where I'd make the checks I referenced at the coil (battery voltage and trigger signal).
 

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I have a 1999 dodge dakota with a 3.9 v6 magnum. The motor was replaced with a rebuilt one and it is sound and tight. However, the truck will cut off and not start until what seems to be after it cools down some. Then it cranks runs perfectly for awhile and then again shuts down. There is a lot of excess heat under the hood but the truck is not running hot. I have installed a new crank position sensor, tps, iac, temp sensor, etc. Point is nothing stops the problem. Once it cools down it runs perfect until it gets to a normal operating temperature and repeats the problem. Anyone have a clue to what this issue is?
I had a very similar issue with my ‘98 and same motor. After lots of diagnostics, ignition parts replacement, and more, on this forum it was suggested the PCM needed repaired/replaced. I chose to replace with a remanufactured part. Problem solved.

After doing some post-fix research I found Dodge apparently put the PCM for that series of trucks in a place where heat would be higher than the PCM could take over the long-haul. Heat over time = failure. So, the heat (causing PCM failure) may, in fact, be the reason for your symptoms.
 

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Had this problem with my '93 3.9. Ended up being distributor module.
Distributor module?
Are you referring to the distributor pick up coil (also, I believe, known as the cam position sensor) that lives under the distributor cap?

Or do the earlier daks have an actual ignition module attached to the distributor like a Ford Taurus I once owned?
 
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