Find someone with an infrared temp gun you can borrow. (Cheapest one at NAPA is 69.00 or harborfreight.com is pretty cheap). Check the cylinder temperatures at the exhaust manifold (right side of engine) with the engine idling. If you have a true miss, one of the six cylinders will show significantly less temperature than the other 5.
The temperature should increase about 20 degrees per cylinder as you move inward from the front of the engine (decrease 20 degrees from center of engine to back) if everything is running properly. If one cylinder is 100 degrees and the rest are around 200-250, the cool cylinder is your miss.
You then must scan the computer with the reader to see if the injector is receiving voltage. If the computer is not detecting a miss, then you must pull the valve cover and inspect the cool cylinder. Check for any broken valve springs, retainers, sticking jake brake, etc. Just because it was rebuilt does not mean things don't fail.
Pull the suspect injector and compress the cylinder with air (with all 4 valves closed-MAKE SURE BATTERIES ARE DISCONNECTED AND ENGINE IS BLOCKED FROM TURING OVER) If you hear air leaking from the exhaust or intake, you have a problem in the cylinder head and it has to be removed. If you hear it leaking heavily into the crankcase (through the breather), the rings on that cylinder are either broken or did not seat.
Is your check engine light on?
Quick way to check for air in the fuel is to get an in-line sight glass from your local Cat dealer (or find a mechanic who has one), install the sight glass between the fuel transfer pump and the secondary fuel filter (should be right in front of the ECM on the drivers side) and run the engine. In reality, you should see clear fuel with no large-foamy bubbles. If you do see them, check all fuel lines on the suction side. It is a great idea to replace them anyway on a truck that old.