I think this explains it best:
The pump timing mark will line up with the crank every 3 revolutions. However, to get the entire system in the correct timing position it will occur every 6 revolutions (where crank is 90 degrees after TDC, cam pins lined up and IP [injection pump] is pointed at its timing mark).
So,it is not necessary to worry about which cycle the pump was in when you took it apart, or its original position, just time/align it to the two marks with the crank 90 deg.s AFC and cam pins inserted, then it will always be correct and will put one of its 3 cycles right where it is supposed to be as long as it is aligned to its timed marks even if it is 1/3 or 2/3 rotations out from its original position it will still always be properly timed for the pulse cycles.
IP pulley is turning 75% slower than crank pulley! IP makes a fuel pulse 3 times per single complete pulley revolution @ 120, 240, 360, 120 degrees.
Injectors fire every 90 deg.s of crank rotation, so IP is making a pulse at every injector firing event @ 90, 180, 270, 360 degrees.
This is the math:

Bottom line, time the dang thing!!!!!

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