This is an old post, from TDS I believe, about the procedure you need to follow. It was written up because you're not the first to do this.
*********************
I just remembered that on friday when I went over to visit Paul at DAS he mentioned to me a way to get the pump gear aligned once the cover has been removed that sounds a lot easier than screwing around with a flashlight and mirror on a stick and stuff.
What you do is lift off the injection pump cover and then the gear. Find the "y" mark at the bottom which points to the tooth that is supposed to align with a dot on the cam gear below(the one you can't see when it's assembled. From that tooth, you count up the gear towards the top on both sides 19 teeth. Put a mark on the 19th tooth on each side, then scribe a line between the two. This line will now run across the front of the gear, and be just above the deck when the gear is lowered into position. You can easily tell if it is out one tooth or not as the line will not be level with the top of the block. You can then lower the cover onto the gear all the while watching the mark to see it doesn't move. Too easy!!
Should look kinda like this.....pic here..
Hope that helps someone, I haven't tried it myself yet, but you can bet I will soon.