OK, I can give more info, the truck doesn't run bad once running, about 10-15 minutes into a drive it will start to buck and cough occasionally. It only smokes when it stalls. When it is cold, it will be hard to start, but once started, runs OK until it starts to buck. I t will buck a dozen times, then smarten up for 5 minutes, then it will stall whenever you try a hard acceleration, even in neutral. Then it can run fine for a bit, then start to stall. It will do a hard start, with black smoke on startup, 5-10 times in a row, then run fine, idle fine to get back to the shop. This wa my test drive yesterday with all the monitoring stuff on it. We had checked the timing key on the pump when we installed the first reman pump on it, but never the crank key. You state it "always runs bad" but this one will run poorly with one symptom, then run OK, then later have another symptom, then run OK again, and so on. It is never the same thing all the time. And watching the datastream (which seems to be quite limited) on our OTC Genesys scanner never shows anything, no codes are set, we did have a P1689, loss of communication b/t ecm and fuel inj. pump.
Let me know what other info could help you help me- thanks, Jack