Diesel Bombers - 1993 Ford f250 7.3 non turbo random misfire part II

OK, I see my first post stumped everone! Lol, But I got part of the problem fixed, I put new glow plugs in it, checked the tanks, and found that the front tank is very clean, while the rear tank is rather murkey. I put new glow plugs in it, it fired right up, then settled into a smooth idle............for about a minute..... then it started it's "stuttering" and random misfiring, with 5 to 15 second smooth idling in between, I took it down the road, it has a little flat spot when you first step on the throttle, like there is air in the system, when you give it partial throttle, you can hear the injectors, if you push down on it harder, you don't hear the injectors, and it starts rolling a ton of black smoke, ease out of the throttle some, till you hear the injectors again, and the smoke stops. I had pulled over for a minute to answer a call, then it idled for a minute or so, then died, it refused to start back up, popped the hood, the ThermoKing fuel pump bowl was full, I checked the schraeder valve on top of the filter housing.....NOTHING ! I took the feed line off the filter housing, and turned the pump on, though it was full, it was not pumping ANYTHING ! I sucked on the hose, and finally got a little fuel to come out, it trickled for a few seconds, then NOTHING! The top of the pump was so hot you couldn't even keep your hand on it. After it cooled down for about an hour, it started. Today, I put a mechanical pump back on it, and another inline clear filter, and a new fuel filter, and disconnected the Thermoking electric pump, no more fuel lines going to it, fired it up, and it ran PERFECT !! ..........for about two minutes, then back to the erratic idle, and random misfires, and no power under acceleration and lots of black smoke. BUT !! My little clear fuel filter is full at all times! Bad injection pump? Anyone? Thanks in advance for any help !