I haven't replied to this one because I thought you were talking about the chain jumping one or two teeth.
Now that you are talking major engine work, I am confused. Seems to be the morning I guess. If there is only a retarding of a tooth or two, I doubt that anything was damaged. I also think there is a good chance the pump is still in time.
The cam is so easy to retime that I would do it and see what you have. You can't hurt anything more by doing this.
BTW I have racked my brain trying to remember if I have ever seen this and I can't remember ever seeing it on a diesel. I saw it once on a V8 though. Its easy to explain the cause on a V8 (although the failure by only one or two teeth - I consider a miracle of religious proportions).
If you are one to two teeth off because that just happened to be where it stopped after running all the forms of retard and advance that occurs when things aren't attached properly, then you would have broke the cam or bent a bunch of valves. If you still have even but low compression it is because of the timing issue; NOT because of damage.
If putting the timing right fixes the compression and the running, I would pull the sub pan off and look for something that could have rolled through the chain. I also would hand roll the motor over viewing as many gear teeth as possible. Watch the chain tentioner rail while cranking the motor. If there is something on a gear the rail will be shoved back as the chain tightens when it rolls over it.