Okay well after reading all of that I have no idea what my issue is I have a crank of a few seconds (1-5) when it hasn't been run in a day or more, then she'll fire up. A few seconds later she starts rattling all to hell, sounding like a misfire or I don't know what. I kinda assumed that was air getting in by my o rings on the return side, which I mislabeled as "air intrusion". It goes away after a couple minutes but it has been getting progressively worse over the past few months.
To be clear this rattling or misfiring or whatever happens intermittently over those couple minutes. Used to be if I bumped the pedal it went away for a bit. That doesn't seem to happen as much anymore.
Sounds to me like you might have a very minor drain back problem. So minor it doesn't stall, but the little bit of air you do have is causing the noise.
After that, it doesn't do it the rest of the day it from what you are saying. If you let it set for a week or 2 before starting, I bet you will get a stall as more and more air gets in. If you want to try an experiment, and have the terrain to do it, if you park the truck with the rearend up hill as much as you can, then see if the problem goes away. If you get the tank elevated, the fuel will have less tendency to "drain back" to the tank.
As far as permanently fixing it, it might be difficult. You have a tiny leak somewhere. You need to take a flashlight and carefully inspect all the return caps on the injectors. Any bit of dampness with dirt sticking to it will be the culprit. If you can't tell, spray it down with brake cleaner to clean it off and then keep an eye on it.
Another common place to look is the fuel heater on top of the fuel filter assembly. Any slight oily dampness will be a problem. There is a couple of youtube videos on how to change the o-ring on the heater, that worked for me for a couple of years and then it started leaking very slightly again. So I read of a guy on here just packing jb weld around the heater fitting so I did that and have not had problem since.
Also inspect all of your rubber lines. I had one that came off the injection pump and ran over to the return system, and it was a little damp around one of the clamps. Had to redo that one also.