Have you installed new fuel filter and new water separator filter, yet?

Do you have a fuel pressure guage to install?

Have you "bled" BOTH the injection pump AND fuel governor for any air in the system?  (use a 9/16" wrench or socket)

Does your fuel hand priming pump leak fuel, when using it?  (If so, it needs replaced)  Note: 3208 fuel system is mostly "suction"; thus "sucking air problems" are very common)

Have you tried sucking diesel fuel, using a short hose, from a clean 5 gallon bucket of diesel fuel? (this is to eliminate the truck's fuel system and hoses, for trouble-shooting and testing)

Once you feel you have the "air" out of the fuel injection pump and governor, and with engine idling; you can use a 3/4" end wrench and start to "short out" cylinders and listen for changes and see if each cylinder "misfires" evenly. {Note: for this test, you must feel comfortable you have SOLID diesel fuel in the system = No Air, otherwise results are basically worthless}

With engine OFF; while using a good fuel hand priming pump, and while hand pumping/priming; you can take a good flashlight and shine it at the governor's throttle shaft (where it enters the rear governor housing)  and look for leaks or bubbles = common failure for an old lip seal, to "suck air" in that location. {Note: a person can built 100 psi, just using a CAT hand priming pump}

Might need to buy some clear hose and fittings to use as "sight glasses" for testing for "sucking air" for the diesel fuel supply going into fuel injection pump. (Again, sucking air is a typical culprit for a CAT 3208 engine, and many times it is caused by too much fuel restriction, before the diesel fuel gets to the injection pump  = old restrictive fuel filters, water separator, old fuel lines (collapsed internally)