Best bet in a run-out situation is to have a working primer pump.
In either case (a run-out or repl. filters) remove the main filter and fill it with fuel (need a wrench to remove the filter) then with an assistant cranking the engine (30-45 seconds at a time) loosen up the injector lines and retighten one at a time, you will see foamy Diesel fuel coming from between the line and fitting, this is the air coming out. What I mean is loosen #1, let some froth come out, tighten it, go on to #2, loosen it, froth, tighten it, go on from there. Try to be quick, you don't want to crank much more than 30-45 seconds, bad for the starter and wears down the battery. Eventually it'll kick over, keep doing it (bleeding air)til it runs smooth, well, you know, for a Diesel. 'Bout normal, you know what I mean.