Wanted to update this for the future for people who search - Truck still isn't completely fixed - Found a black algae substance in the fuel filter housing. When the truck was running nothing was coming out of the fuel filter bleeder on bottom so I poked it and it shot a bunch of junk out. I assumed this would only cause a no start (if bad enough I'm sure it will) but it also added some difficulty to my truck starting. I misspoke earlier - I was looking for a check ball, and then found the check valves inside the governor. Everything is functional, spotless and clean fuel system wise. The truck is stored in doors in a heated garage and has been maintained well. Truck does start significantly quicker now, but is still far from right. Will crank over in 41 degree weather after 15-20 seconds. Runs poorly with white smoke until warm.
Conclusion - At this point after googling "Cat 3116 white smoke on startup" after all the checks done here it's most likely the injector cups need reaming and/or the rack needs set as well. I need to verify the return line air bubbles and fuel pressure. Been searching on how to do this, but it looks like a lot of specialty tools are needed. Maybe some of that black algae appearing stuff is up in the injectors and will clean out over time? No idea.
Process done -
Checked tank for debris (none) and removed fuel pickup to make sure its free and clear. Diesel fuel is brand new
Installed new check valve on fuel tank pickup
M35A3 fuel tanks are not pressurized with air (that's a breather) and don't have an electric pump
Blew air through the fuel feed/return lines to make sure they're flowing easily
On the Governor - check feed and return check balls for free movement and trash
Checked all O rings for tears as well as the plastic regulator inside the return fitting on Gov.
Open Fuel filter housing bleeder and cleaned debris, algae, by fuel pressure shooting the junk out.
Truck does have significant air system leaks from age but never warning buzzers.
