Here's a blast from the past. I've been having ongoing problems with this damn engine. Anyways, I took it into a mechanics to take a look (actually, this is the third mechanic I tried, the rest were absolutely useless).
I'd always suspected the timing might be an issue and turns out it is. The interesting thing is, the injection pump appears to have grown larger when it was rebuilt, it simply cannot be pushed down far enough to get the timing right (which is what I originally thought). I called the shop that rebuilt it, and so far they have no possible idea on how that could happen. The mechanic has even tried taking the roller off another pump in case somehow the wrong one was put back, but no change.