ford transit 2.5 turbo diesel pump timing ?

how do i set the timing on my Ldv with a 1999 2.5 ford turbo engine which was fitted with a fly by wire system but because of it going into limp mode I have changed it to a cable on a bosch pump from a similar engine but it wont start now. I have put a live cable to the pump and removed the key tag part from the pump. I have bled the fuel system and have fuel at the injectors but feel that there is too much play in setting the pump timing as the bolt holes are slotted. I feel that this could be the problem. how do I set it right? please help.