N14 Celect Plus Misfire and Gray Smoke

I can confirm it's a programming thing, cummins dealer said it's a feature fleet managers can have enabled to prevent a driver from unplugging the speed sensor and bypassing the governor. Also found my dead injector, it's currently in hole 1 with a exhaust reading of 160* at idle and all the other at 220 to 230. The misfire has gotten weird in that at start up its completely gone, but once the truck warms up or you drive it, it become super apparent and the truck shakes under power. I'm going to replace the bad injector but I think theres an issue with the harness for hole 3. Unplugging it doesn't make the truck stumble, but plugging it back in the truck gains a couple hundred RPM. Could that also be a bad injector even though it's at an equal temperature?
Thanks for all the help so far, the truck idles way smoother then it did before now, the smoke is mostly gone too.

 

I'm going to swap the injector tomorrow most likely, just been putting it off because of the pick you need to pull the injector out broke on me.
I've noticed that the longer I run it the better it sounds, not sure if that's placebo or the fuel conditioner I added. Right now, I think there's an issue with the ECM check valve because the fuel filter was empty when I pulled it and it takes about six seconds of good fast cranking to start up. Like it's losing it's prime and having to pull fuel from the tank every time. Any other trouble spots that can get it to lose a prime a couple of minutes after being shutdown?

 

Both gaskets are there, I found a thread here of someone having the same issue, so I'll be following along there. Thanks for the help.
I still haven't been able to get around to swapping the injector, but planning on doing that today as soon as I get the truck back from inspection.

 

New symptom time, and maybe a solution to the previous problems. Tried driving the 13 miles from where I've got it parked to the inspector so I could get it inspected and it started acting like it was choked for fuel, started missing, and then would die. Let it cool for a few minutes and all if a sudden it would start back up with no problems whatsoever, throw the high idle switch on and a few minutes later it would do the same thing and stumble and miss then die. No check engine, stop engine, or engine warnings whatsoever and I've checked to make sure the bulbs work. I've got a new engine position sensor and am going to throw that in and see if it improves the issue of long starts and the stumbling when hot. It's got me wondering if this miss I've been chasing has really been the engine position sensor.