Is there a water separator in that system back at the fuel tank?
Who's fuel filter cartridge are you using? Is that the only thing you changed?
Are you getting good flow to the filter housing? Remove cartridge and check or disconnect line to the filter housing and check for flow. Back blow compressed air into the line back to the fuel tank.

Hi Team,
how long does the engine run before it shows the out of fuel condition??

If the engine runs smoothly for a period of time them begins to miss from air ingress or lack of fuel then I would suspect some blockage at the fuel tank pickup pipe that floats away until expected higher fuel flow rates experienced with the engine running cause the the obstruction to be sucked backed back over the fuel tank pickup pipe.
Sometimes pieces of plastic that cannot easily be seen thru the fuel can do this--CCJ spoke of a clear flashlight lens in a truck fuel tank that was hard to see and caused mega headaches for sometime and many checks by other people over time until he found it.

If the engine runs rough from the get go then you may have crud between an injector needle and seat or a sticky needle from crud introduced when changing the fuel filter that could be allowing combustion gasses back into the fuel gallery
--I recall that I once found a complete unopened box of engine oil filters that were contaminated with processing swarf way back when I was an Apprentice at the Dealer.--Point being, always check inside a filter inner tube before fitting it--luckily I was taught this at the Dealer.
Another source of contaminants when changing a fuel filter is to pre-fill the fuel filter using dirty utensils and /or fuel down via the inner after filtered centre tube.

EDIT
Also agree with OM's idea of the new fuel filter possibly being major thing changed and so would check the canister seal to the filter base is compatible and so is effective.
I have now found a flow chart in another publication that address air in the fuel but not "NO fuel".
Will digest the chart further to see if there is anything to be learned from it.

Cheers,
Eddie B.

I tried it again today and replaced the fuel filter (napa) and purged the fuel line w/ compressed air, it ran great and didn't bog down for about 10 minutes, then it lost power and died. No fuel from the transfer pump when pumped. The old fuel filter while relatively new (put on before the winter) was absolutely disgusting. I'm starting to think there may be something blocking the fuel line in the tank, if so, how would I go about finding/removing it?
Thanks
Josh

Are you getting a black gooey looking material in the filter? Could be a case of Algae growing in the tank.

no goo, just very nasty diesel with small chunks of crud

I think I may have figured it out, the main fuel line had a major kink by the fuel tank barely letting fuel out and it also had damage to the outer casing of the line. I need to replace it. I don't think there is a blockage in the tank because when I removed the line fuel gushed out like it should. I'll see if a new unkinked line will help.
Thanks for all the help
Josh

New fuel line and it seems to be working, I can feel fuel pumping through the line, don't want to jinx myself though.
Thanks for all the input and help
josh

May be short lived until you get all the junk out of the system.