Greetings,
You have several possibilities here.
First is that you picked up a batch of bad fuel, possibly contaminated with water or algea. I would suggest draining the fuel/water seperator and then replacing the filter again. If it helps for a little while then starts again with the same problems, do it again but add a batch of diesel fuel treatment as well.
The second is that your new lift pump may be on the fritz. Possibly a bad connection or ground and it is only intermittently working.
The third concerns the PMD and fuel injection pump. When you replaced the PMD (aka - FSD or Fuel Solenoid Driver), did you also have the FI pump replaced or rebuilt? If not, then you may need one. One problem is that excess heat from the FSD can also bake the optical sensor inside the pump which will fry the pump and require a replacement. In addition, the heat from the FSD also thins out the fuel which reduces its lubricity and accelerates wear on the FI pump and will also lead to a replacement.
I always recommend that whenever anyone installs either a new FSD or full FI pump that they remotely mount the FSD off of the pump body onto a device known as an "FSD Cooler". This is nothing more than a finned heat sink that the FSD bolts onto and is mounted somewhere away from the FI pump. With this, the heat from the FSD is bled off into the atmosphere and not absorbed into the body of the FI pump causing all of the problems I just mentioned.
The DS4 electronic fuel injection pump is actually a pretty good unit and worked very well on the test bench. But drop it into the V of a diesel motor, keep the FSD bolted to the front and then cover the whole thing with a plastic "Turbo Diesel" cover and you have a formula for heat-related problems. If you end up replacing the FI pump, throw away the plastic cover and remote-mount the FSD.
Cheers - Jonathan