07xx is a generic transmission OBDII code. 17xx would be Chrysler specific. If there are no other codes present, the book will point toward incorrect voltages, ie., bad connections, open circuits, short to voltage, short to ground, sensor resistance outside of the approx. 300-1200ohm range. Failing sensors can get wonky when hot it seems. Intermittent problems (yours won't set the MIL) sound like wiring.
Seems possible to monitor the speed sensor voltage the PCM sees with an analog VOM looking for small spikes a digital VOM can't display.
What happened with the varying idle voltage (flickering lights) and fuel pump pressure? Did the rail ever hold pressure?
I've no idea how to how to deal with an IAC issue, but physically restricting the orifice or maybe fooling the PCM with a small resistor might be a workaround.
That condenser/capacitor by the coils most certainly should exist, my '99 has one. That circuit, A142 is ASD relay power to the coils, injectors, and PCM. I'd be also curious to see what voltage the PCM is seeing at any given time, especially during malfunction. I read this thread from time to time because it's interesting, and you seem capable.

 

Idle fuel pressure issue was solved with a new battery temp sensor. I haven't run the truck in the dark yet to check the lights. Battery temp sensor was 12.8k ohms, FSM called for 9-11k ohms. Map sensor helped throttle response and improved the bog/backfire. New 02 sensors smoothed the idle and allowed it to idle well when hot (with the new map it refused to run when warm). I replaced the output sensor on the trans and the code hasn't come back yet, it also did improve the idle while braking, it seems less likely to stall. I did some data logging with my X3 programmer and you can see the in the map readings as you are coming to a stop the vacuum decreases for the last few seconds implying the IAC is opening. Map is reading about 14.5in Hg at idle. Everything up to this point has helped but still have yet to find the smoking gun. It is almost like a vacuum leak. I may smoke test it again, but with the throttle body off and a plate to isolate the intake manifolds. However that won't be for a week yet.

Also thank you for the compliment. Where is your capacitor attached to? I forgot to document it and just have it attached to the coil mounting bracket bolt.

 

So I did something unorthodox. I Disconnected the main vacuum port for the vents/cruise and plugged the line. No more stalling. The idle still drops to 500rpm and runs rough when coming to a stop and then picks back up to 650rpm where it should be. Still bogged a little with some occasional backfiring then took off. That's the best its ever felt when it takes off. Now I'm even more confused. I think I may have an issue with the new IAC, which Hey You eluded to already. However still something mysterious. I even took the top off the ignition wire track and made sure all the wires were separated to verify no crossfire.

 

Wonder if your map sensor isn't calibrated quite right......

 

I do have access to a pressure sensor at work. I can compare it to what the pcm is reading. I may borrow the sensor for the weekend. At least to make sure its the same at atmospheric pressure.

 

I keep forgetting the pressure sensor however I did do a couple things.
1: Improved smoke test. I made a plate to block off the throttle body opening. No smoke from any external leaks (yay I found and fixed all the broken lines). However there was smoke pouring out of the breather in about 5-10 secs. That concerns me.
2: I sent my datalog to the tuner. He said most likely I have a vacuum leak.

 

How are you smoke testing the truck?

 

At a shop my friend works at. Used a professional pressurized smoke machine attached to the brake booster line. We blocked off the throttle body with a plate and smoke for 10mins. Only place it would come out is the breathers/oil fill. We clamped off the breather to the air box after smoke came out of if (air box was off).

 

That's normal as the breather (not PVC) is just that a breather. The only other place I could see a vacuum leak would be where the airhat meets the throttle body

 

I might be tempted to take a peek into the manifold, and see if you have oil pooling in there......