First, fill in your signature so you don't have to tell us on every post what your truck is and what equipment you have added to it. (User CP -> Edit Signature)
The ENTER key makes it possible to split your post into paragraphs, which makes it easier to read.
So... if I'm reading this right, you have a truck that you felt was smoking too much, so you had the dealer flash it back to stock to be sure it wasn't a latent program in the ECM.
Despite that, it's always taken a while to get started when it is cold outside.
When you did get it started after this and forgetting to leave the block heater plugged in you got some black smoke, not much, but some... and it lasted about 30 seconds, and then you got white smoke for about 20 seconds.
You don't need to unbolt the FCA for the test you're talking about (in fact, DON'T). Simply disconnect the connector from the back. The torque spec for those tiny machine screws is in inch-lbs (i.e. just snug, you're holding it in place, not trying to cram it into the hole).
Your banjo bolt, if memory serves, needs about 18-20 ft-lbs.
The white smoke is reason for concern, as it can be caused by a number of factors... water in the combustion chamber (blown head gasket, will also cause a hard start), leaky injector stuck in the "on" position causing unburned raw fuel to go out the exhaust. If it's the former, you'll find water in your oil and oil in your water. If it's the latter, you'll smell raw diesel fuel at the exhaust.
I'd say check first for the water/oil condition, second for the diesel smell of the white exhaust, and third the rest of the things on your list.