I left the pump on my engine when I redid my head gasket, but anyway. THere should be marks on the flange of the pump and the back side of the gear housing. If it is the same pump, line up the marks. If there are no marks, here is a basic rundown of how to do it.
1) FInd true TDC. The timing pin gets you close enough to set the valve lash, but isnt consistently reliable for something as touchy as timing.
1a) find TDC with the timing pin. Then back the engine off about 30deg. tighten the intake valve adjusting screw 2 turns. GENTLY turn the engine in the direction of rotation (clockwise as you face the front of it) until the piston hits the valve. Mark the h-balancer in reference to something solid on the engine. (book recommends taking a piece of wire, and making a pointer out of it. ) Rotate the engine back the other way, GENTLY, til the piston hits the valve. Mark the balancer again. Split the difference, and that it true TDC. Loosen intake valve screw and turn engine back to TDC, reset lash.
2) rotate engine to about 25-30 deg BTDC.
3) Remove any injector lines in the way, and take out the plug in the middle of the end of the pump where the lines come out. (If you can get it with the lines still hooked up, I tip my hat to ya). Set up the dial indicator, and make sure to zero it.
4) Turn engine til you reach TDC. The amount the dial moves is your plunger lift at TDC. non-IC engines call for 1. 40mm (. 055"); intercooled is 1. 25mm (. 049"). Margin of error is +/- . 02mm, I believe.
5) If the pump is not where it should be, move it down (AFC away from head) to retard the timing; and up to advance it to where it needs to be. I would recommend rechecking it after adjusting just to be sure. I have mine in the range where a little too far makes me lose bottom end torque.
Daniel