That is just too complicated. If it is leaking until you start it and then it stops leaking and starts smoking that would tell me that the pump can't keep up and the injection pump is sucking air. You have mentioned a water separator several times and these trucks did not come with a water separator originally so I am guessing there have been a lot of modifications made to this vehicle. unless you are talking about the filter on the firewall. First the smoke, White smoke is unburned fuel, as in when it is cold. blue smoke is oil and black smoke is excess fuel. The lines, if it is a rubber line then replace it, no questions, just replace it. Make sure all of the return lines on the injectors are good and that they are not kinked all the way back to the tank. Lastly, whoever said that if your injection pump is not bad yet plan on replacing it.......................... I have worked on these things both military and civilian plus marine for many, many years and the pumps easily go 200,000 miles with no issues as long as you run clean fuel through them. I had a couple of customers with Blazers with over 350,000 on them that ran perfect. Start trying to run waste motor oil and yea, you will be replacing pumps often.
Rick