I think the pump rod length is for linkages without the alignment hole, my understanding is that the pump leaver must be on its stop and the throttle butterfly closed with all linkages taught so that any movement then opens both the pump and the butterfly at the same time. So, if you have an alignment hole you just lock the cross link and set the rods to achieve this, if you don't have an alignment hole then you must first set the length of the pump rod before removing any play with the others. When you've done all that you just pray that any previous owner didn't move the linkage arm on the pump as that can really mess things up.