You can change the controller with out pulling the pump, its a little more work but it can be done. Even if you pull the pump, the timing marks are on the pump housing and pump itself, just line them back up. Look at the 12:00 o-clock position on the pump mounting face for a small line stamped across both pieces. Also, if you pull the pump, you have to pull all the lines off, don't bend them out of the way!
Check on some of the diesel site on the web for information on relocating the controller. Heat is what breaks them down. We have mounted some in a heavy heat sink out on the valve cover with good results. The new issue of GM controllers is different then what was issued on the truck, and we have had good luck with these as well.
Joe