different type of injector pump wires ford transit 96?

hi i wonder if any one could help i have recently changed my engine in my transit as the old engine had lost its performance. the replacement engine is in great condition and i heard it run before it was removed. the problem i am having is that the wires from the injector pump are different to the one i removed ie 3 wires instead of 1. how cam i over come this !!!!! please help.