A couple tips and then some knowledge for everyone:
Re-timing the fuel pump is as simple as lining up the pump timing mark with the mark on the inner cover at about the 8 o'clock position. Doesn't matter which rotation, and it doesn't matter how the pump will only line up every third engine rotation - this is normal.
Pumping the plunger on the fuel filter WILL NOT FILL THE RAIL because that is on the high pressure side of the fuel pump. If you really want to be tricky, unlock the #4 fuel line a bit from the rail, and rotate the fuel pump yourself. It will fill and push fuel out - then tighten it up and you should have vroom a lot quicker.
Now - about the timing of the fuel pump. The rail is ALWAYS full of fuel, what you are doing is managing the pressure waves with the fuel pump timing. This is a 4 cylinder engine, so how can the fuel pump possibly match with only a 3-lobed pump? Its a little thing called MATH.

If you take the size of the camshaft pulleys as "1" then the crankshaft is "1/2" and spins 2 revolutions for every ONE of the camshaft. That is how it can be a 4-cycle engine, and why it takes TWO revolutions to return to 90 ATDC on #1... On the intake stroke.
So if the cams are "1" and the crank is "1/2" and running twice as fast... The fuel pump is "2/3" and is running 33% faster - So that each and every time one of the cylinders opens that pressure drain (the injector) from the rail, the lobe of the pump could be lined up perfectly to push fuel and maintain the rail pressure as almost static and smooth.
If the fuel pump isn't lined up, the rail pressure will plummet when the injector opens, then the fuel pump will be pushing against a solid wall with the injector closed and the rail pressure will spike. As the rail pressure drops, the spray pattern from the injector will be uneven (think about shutting off a hose rather than letting go of the spray trigger) where the spray should be mostly constant with the timing properly done.
You don't want the pressure in the rail to spike and droop, that puts added stresses on the fuel pump and just generally makes the engine unhappy and louder. Sure, it might still run... But isn't a precisely running and smooth engine better?