Might be the case. The correct way to install the pump bolt and lock nut is to install the pump with out the lines, Turn the pointed bolt in until it bottoms out and the pump does not move. Then back off just a bit. the pump should wiggle just ever so slightly. Tighten up the jam nut and then install the lines. The pickup does get pre installed onto the pump. Make the lines meet the pump as opposed to forcing the pump in to accommodate the lines. You really should not have any interference with the no. 5 rod and the pick up tube.

Mike