You don't want to take any part of the Injection Pump apart to time it, just loosen the 3 bolts up on the round flange of the injection pump, where it attaches to the gear cover that has the oil fill tube. If you are going to try and turn it yourself, try moving the top of it towards the driver side for safety reasons, only move a little at a time and never try to move it while it is running.
BTW I just got your PM, my truck has 36 12.50 16.5 military hummer tires, the only lift I have is a 3 inch body lift, it will rub the springs just a little if I turn it full lock.
Also is your trucking running or just cranking when it is making this noise, either way either is going to make it really noisy, but if you already got it running it is going to sound even worse. I am just curious if you were using either to keep it running or just to help it start, either way is not ideal but many people have done it, I even witnessed a friend either his 97 Powerstroke and then blow the air filter box off of it when it was ignited by the heater. I told him not to do it but he said he had done it before with no problems.
Maybe you can take a video of this and post it so we know exactly what you are talking about, but as Mel said if it only does it with either then I doubt the problem is your IP.