A copy of my post from the 94-98 powertrain forum...
Heres a very 'simple' way to set your timing back to stock (or whatever the pump has been set at if it has been rebuilt and the pump timing altered)
First off, bar the engine over to #1 TDC where you will be able to lock in the pump gear timing pin (see pic below). the timing pin is located just below the injection pump.
Now, if you are lucky and the timing as not slipped you will be able to pop the plug off of the side of the pump and pull out its 'timing plug', on one end it just has a little metal 'tit' that faces inwards towards the pump for normal operation and on the other end it has a plastic part with a notch cut into it that engages a timing arm inside the pump.
When you pull the plug out of the hole you should be able to see the arm in there and should be able to flip the timing plug over and have it fully insert into the hole and the notch line up on the timing arm. If you cannot see the arm your timing is way out to lunch, if you can see the arm but the timing plug wont go in properly (very close but wont go), the timing has slipped a tad. at that point its your call if you want to reset it or not. (IIRC appx 1mm of movement on the arm = 1.5* timing)
This is the location of the pumps timing plug (basically between the pump and gov housing) and its orientation for normal operation.
this picture shows the timing plug being flipped around and locking to the notch on the timing arm inside the pump
At this point if you decide to reset the timing, MAKE SURE THE TIMING PIN ON THE GEARTRAIN IS DISENGAGED!
Then while watching through the hole in the side of the pump, bar the engine over till the arm is centred and you can engage the timing plug fully.
Now, for the sake of not breaking that plastic plug accidentally, remove it. Then procede to remove the pump drive gear bolt (its tighter than a mofo!) and use a puller to remove the gear. you may want to just quicky double check the timing on the pump didnt accidentally move before pulling the gear.
The puller required is a '2 bolt', their are specialty ones sold (i have one), but have been told any puller will do.
Now with the gear loosened from the shaft, get in there with some brake clean or some type of cleaner that LEAVES NO RESIDUE!, this is very important, any bit of gunk or oil on the shaft WILL cause the timing to slip.
Then, bar the engine over till the timing pin will engage in the gear. Now hand tighten the nut onto the pump shaft, disengage both timing pins, and while holding the engine from spinning (hopefully using the proper barring tool!) you can tighten the pump shaft bolt to 145ft/lb
Now, in theory, if you engage the timing pin on the geartrain and pull the plug out of the pump you will be able to see the arm in there and engage that timing plug. As long as nothing moved while you were doing this...
I think that about covers it, i know this topic pops up every once in a while so i hope this helps some of you!
Last but not least.... DO NOT FOGET TO DISENGAGE BOTH TIMING PINS BEFORE MOVING THE ENGINE, YOU WILL BREAK THEM!!!!