First thing is air itself will cause rough running. That should be eliminated. Is this the primer pump known to leak and draw in air? If so an easy fix & repair kits aren’t to expensive. Open the filter and examine for water, bugs, and that it is sealing proper to not cause the air intrusion.
Just sitting - how long?
Humidity- how full was the tank?
Modern diesel has ethonal/methonal which will outgas from the fuel turning diesel into lower power fuel like old gas that sat for couple years used to 20 years ago. Also from the ethonal/methonal they cause any of the moisture present to be absorbed into the fuel and harder to separate or set off the wif alarm.
On the flip side if alchol free fuel, it sits in the tank separating and sinks to the bottom, getting sucked in all at once and ran through injectors if water seperator isnt working - like the water absorbing all in one fuel filter is already “full” of moisture in can handle.
White smoke is either unburned fuel or water being steamed. A third item that has seen to create any color smoke is different algeas (bugs) in the fuel. Either way the safest answer is drain the tank and go with new fuel. You need to save the fuel and let it settle to see if water was in there. If no water then it can be mixed back into the fleet.
On the subject of a water - we just had 2 days of non stop rain here, which most of you would even consider a rain, just heavy drizzle. Followed by 12 hours of fog, 100% humidity. A day later it’s 94% humidity. (More rain than last 10 months combined). It only happens here about once every 8 years would be my guess. But soon we will be back to Dust in the air like normal.
Also having worked for 1 of the 2 major fuel suppliers for this area, I got them to install the most advanced water separator systems for distribution there is and saved them long term money doing so. Our “competition” is friends with a half owner of our company and they discussed it. Last I heard as I left the company, they were installing it also. So water in fuel in Vegas area is just not a concearn almost ever.
But my friend, my older Sister lives in Idaho (Jerome) and she and her husband are truckers. Stories I’ve heard over last 20 years- plus iirc NW Kansas is higher humidity yet, so you probably get water in diesel all the time. I’m considering an aftermarket water separator just for road trips. If I lived and travel where you do- every truck would get one.