Could running water lines and electrical conduit along the house ceiling possibly hurt the effectiveness of my ventilation system?
Yes, indeed. During minimum or transitional ventilation, we want incoming air to stream along and hug the ceiling as long as possible, in order to get good air mixing. If pipes and conduits are placed on the ceiling above air inlets they can appreciably obstruct that good airflow stream, cutting its velocity down and directing outside air downward toward the birds. Alternative locations for water lines and electrical conduits should be found.