Take off the gearcase cover, line everything up (cam, crank, pump. . ) and mark everything up with a paint pen to make sure it goes back together the right way...
The pump gear is keyed so you can't put that on wrong... just make sure you line it up when you put it back together.
Since the VP-44 is electronic... you can get it within an earshot of being 'dead-on' and it will figure out the rest.
There is a sensor that reads a reluctor wheel position inside the pump on the pump shaft called the 'angular encoder'. That provides input to the pump's ECM as to where the driveshaft is.
The ECM can then tell the other solenoids and so forth what to do to affect timing and make your truck run.
Matt