the other day i was looking into my dads pump to try and solve the leaks (this was before i had a assembly drawing) and removed the top cover off what has turned out to be the diagram push rod, i then picked this up to see if i could see any damage to the seal,thats when i went oh FCUK

at this stage I'm taking the logical path and was going to make some marks beside the top of the seal and then try running at each mark until i can find out roughly where it should be,ie from 12-3 or 3-6 or 6-9 or 9-12 then make more marks more accurately and try to tune it up more
or am i just wasting my time and potentially going to kill the motor
any help appreciated
my dad has no funds and just lost his job hence why i'm fixing it and not a diesel mechanic so yeh