A few months ago my awesome boss gave me a truck. He knew I had been drooling over all of his 2nd gen trucks for years and he hooked me up! Anyways it's a 98 1500 4x4 with a 5.9 gasser and an automatic. I have been a general line mechanic for 30 years and I thought I knew these trucks well but my very own is kicking my ***.
When I start the truck in the morning it throws a crank sensor erratic signal code instantly and since I've already changed the flexplate and the crank sensor I'm thinking the pick up coil might be bad or I have a bad plug or wire because it idles like a carbureted motor jetted too rich then off the line at a light it bucks and backfires like the usual ignition miss so I open the distributor and wiggle the shaft and its fine. New motor six thousand miles ago so new chain and gears too and I watch the waveform pattern on the scanner of the cam sensor/ pick up gadget and it is beautiful. Smooth and right inside parameters. I got new plugs,wires, cap, rotor, crank sensor and flexplate and still the same stupid ignition miss. I then scratched my head and bought a reman distributor and it still does it. I have good fuel pressure, iac valve, tps, and map all work and I even tried a new pcm and still the same thing. After I put all of the parts back on my bosses identical truck and contemplated building a large fire under the truck I went home and on the way I looked down and the trans temp light is on and the overdrive off light is on. I have continued to drive it for two months and have learned that the trans temp and overdrive off lights disapear after it warms up, overdrive comes back but my mysterious misfire is always still there. Please tell me you have a better idea than I do because I'm about ready to get rid of the nightmare even after new engine, rebuilt(they said!)transmission and all the parts I've thrown at it. I just put new tires, a lift, a stereo, upholstery, and I fixed every last door ding and painted it. I'm passing this troublesome thing off to hopefully someone who knows more than me. Please help

 

You have more then one problem here. Since you have a good scanner, see what temp the transmission is at when the truck is fully warmed up. Did you check the ignition coil?

 

The sensor in the distributor has nothing to do with ignition, it is used for injector timing, that's it. If you are getting an erratic crank sensor code, that feller is on the back side of the engine, behind the passenger head. You changed the sensor, and flexplate, one would think that would solve it, but, as it did not, couple things to check. First is, what brand sensor did you buy? If it isn't a genuine mopar sensor, then you need to get one, and replace it. If that doesn't solve it, then there is either too much gab between the sensor, and flexplate, or, you have a wiring issue.

 

All timing is derived from the crank position sensor, the sensor in the distributor merely tells the PCM the cam position so it knows which cylinders to ignite and which need fuel injected. Your comment about sounding like it's running rich makes me wonder if the O2 sensor readings are way wrong. Did you look at the O2 sensor readings ? The wiring for the transmission runs down the same harness so if there's some shorting in between it might affect both.

 

Was it a Mopar sensor? I went through 4 different Crank Position Sensors, 1 from Oreileys, 2 from Napa and 1 from Manny, Moe, and Jack. I returned them for my cash back. I finally bought the Mopar CPS and haven't looked back. Same for the Cam Position Sensor inside the distributor.

 

Agree with Mopar sensors if you don't have them. Did you set the fuel sync?

 

The crank sensor is an Echlin from Napa and no I didn't set the fuel sync unless you mean turning the distributor to where it should be for injector timing. I did do that. The codes I am getting over and over no matter what are a p1391, p0138, and a po713 which really confuses me because there isn't a trans temp sensor or wiring that I can see down there. I have seen them on the cooler lines on other trucks. I have checked the wiring even as far as pinning both ends of the wires between the cam and crank sensors and the pcm and looking at the continuity. I can get a mopar crank sensor tomorrow but I will bet that doesn't fix it since I've already tried a used mopar sensor. I just got another brand of cap, rotor, and plug wires and went back to a champion plug this morning and it did nothing for it. I'm so sick of buying parts and getting nowhere. I just transplanted a 5.9 diesel into a 5.9 gas truck the other day and had less trouble.

 

There's a good chance your chasing ghosts focusing on the sensors themselves. All of the codes list wiring issues as one possible cause. One of the quirks with that generation PCMs is that shorting of the 5V sensor supply anywhere can cause all sorts of weird issues. There is a a 5V sensor supply running all the way into the transmission and it can even short inside there. As I already suggested above, check the wiring running down to the O2 sensors and transmission. You can also try to unplug the transmission and see if the P1391 goes way. Note you'd have to shift the transmission manually.

 

If the 5 volt supply voltage gets shorted to ground everything dies including all the gauges. Had the 02 wire rub on the transmission and that grounded it out. You might want to try to clear the memory out of the pcm and have it relearn the sensors. Disconnect one battery cable and turn the lights on or touch both battery terminals together.

 

The problem with the anecdotal story above is that the O2 sensors don't use 5V supply. In fact the sensors create voltage via an electro-chemical process, the 12V power is for the heater only. However it does have a point in that wiring issues along the transmission wiring harness are not uncommon.
The OP's description sounds like the symptoms change as the truck warms up, so it's most likely not a "hard" short to ground. Again, seeing both O2 sensor and transmission temp sensor faults at the same time would make me look closely at the wiring down there, given that swapping sensors was unsuccessful so far.