I’ve been having hell with my ‘99, it’s a 2500 4x4 with an automatic trans. 130,000 miles all stock except for a few cosmetic things. One day out of the blue the trans went into limp mode, I hooked up my scan tool and I didn’t have any communication with the transmission. I started checking wiring harnesses and senors on the transmission. Found the output shaft speed sensor was bad so I replaced it and now the truck shifts 1-3 but has no O/D. It’s not my daily driver so I let it sit for a few days and came back to it when I had some time and I noticed it wasn’t charging the batteries and the A/C wasn’t working either. I wanted to verify that the it wasn’t each system failing at the same time and I jumped the a/c clutch relay and the a/c began cooling. The alternator tested fine so I put an external voltage regulator in the alternator and it began charging. I added a switch to the trans relay and the O/D solenoid engages. I was leaning towards the PCM being failed so I checked the power and ground to the PCM and it had both and no communication with the pcm and no codes so I ordered a rebuilt one ($600) and when I installed it, I still have the same issues. I’m at a loss here, how does the PCM know to turn accessories on?  I was told that the CKP sensor is how the PCM knows the engine is running and turns everything on. I had an intermittent No start, and no tach issue with codes for the CKP sensor so I replaced it with an eichlin part. The engine starts and runs so the CKP sensor has to be good right? I also have replaced the APPS after a no throttle response issue and fixed that. I checked my 5v reference on the ECT and it was fine, that means the 5v on the pcm is fine, correct? Is there a way to check the CKP sensor without a Scope? I had a industry friend tell me that it could possibly be my batteries are toast (optima red tops). They’re old but the truck starts fine. Any help is appreciated, thanks guys. 

Try disconnecting the and cleaning the following:

The three PCM connectors

The engine harness to truck harness connectors (left of brake booster)

The ECM connector, it has a bolt in the center of it.

The ECM sends a pulsing signal that matches RPM to the PCM, that's how it knows the engine is running and can energize the trans, alternator and AC.

@Great work! is right all those systems need to see the tach signal through the CCD network. I'm going to assume you got a P1698 code. Since the CCD network is not talking to the PCM then the PCM doesn't know the engine is running it can't see the tach signal. 
 

Thank y’all both for the help. I don’t have a scope at home to check tach signal, so to test the CCD network can I test at the DLC pins 3&11? Should I use a chassis ground or should I use a ground off the the DLC to check for voltage? With floating ground systems how do I verify that it’s getting ground? I was getting a p1698 code previously but I’m not getting any codes currently. My displays and gauges all work fine, does that narrow down the source of my CCD issue. I’ll be honest I’m a little lost here. I service/build wheelchair accessible vehicles and deal with electrical issues pretty frequently but can-bus issues are normally a factory problem. I appreciate all the advice. I’ll go ahead and clean all the connections and replace my battery terminals and do the w-t ground mod