I am not sure what you mean by your description . The exhaust and intake lobes of the number one cylinder should be about the ten and two oclock position. Or fairly close to it. If the lobes are pointing other places then at least some indication of a fault has been located. I really did not like your earlier description of problems with a rebuilt injection pump.

Now if the lobes are pointing downward you are also on the wrong stroke. With all your issues something wrong in this area is easily possible. The best part is it is labour intensive rather than parts.