Need help with pump timing please!!!!

Hi All, Well yesterday i decided to check the pump timing on my 300tdi what a mistake! I aligned all the marks (flywheel and pump) to find that my pin wouldnt fit into the hole on the pump but the engine ran ok? If i undid the three 10mm bolts on the pump and aligned so the pin fitted it ran like a noisy bag of ****e and was also fully adjusted which made the engine run as flat as a witches tit.I then adjusted the pump to advance the timing to try and get a diesel knock and then back it off a bit until it stopped rattling but it wouldnt start so with no pin fitted i adjusted it so it ran but i now cant get it to run as well as it did before i messed it up so my question is what have i done wrong and why wont the pin fit in the pump when the flywheel is lined up yet it runs?

Maybe the belt is one tooth out on the pump, compensated by using all the adjustment on the bolts.