You could also just swap to a electric pump. I don't think I've seen anyone do it, but you could put a electric pump between the mechanical lift pump and the filter.
I've done this on one truck; it worked I think... The mechanical pump will push fuel through the electric easily enough.
I don't know all the ins and outs of the injection pump, but I believe it has a return line on it, and when the fuel leaks down in the return system, it will drain the injection pump. That is why when you have this problem, the engine will start and run and then stall shortly after. The engine runs on the fuel left in the high pressure injection lines, and then all the air from the injection pump hits and it stalls out.
No, NO, NO NO.
First off, the fuel in the high pressure lines is 'static' - it doesn't move at all without fuel (in the IP) to push it forward. The IP gets it's 'working' fuel exclusively from the inlet side of the pump; what's in the housing is already "used" and serves no purpose except cooling.
When you have air intrusion, the fuel being run on is the small amount in the hard line from the fuel filter down to the IP. That's it.
Back to the original issue: STOP WORRYING ABOUT THE RETURN LINES. They don't even need to exist for the engine to run(it'll just spray fuel everywhere, especially the IP return).
What you need is simple: for fuel to /not/ drain out of the filter, back down the supply line and out.
If you have a solid, new lift pump - it acts as a check valve and prevents fuel from draining back. As they age, they stop sealing perfectly - good enough to pump fuel, not good enough to prevent a small amount from draining back over hours.
The solutions are:
1. Make everything perfectly sealed - from the top of fuel filter back down to the tank. This would be deleting the return orifice, fixing any little leaks, etc.
2. Install a check valve or electric pump in the supply line to the fuel filter. It won't matter how badly anything else leaks, if the fuel can't flow back down the supply line.
I personally would go with option two more than anything; that way you don't have to delete the return orifice(which helps a lot if you run low or out of fuel - getting air when running).