Don't know how you flush the motors. Some boats have a hose attachment to flush. Its a possible spot for air to leak in before intake pump. If impellers and thermostat are OK as well as everyones suggestions and problem persists maybe removing heat exchanger and flush both sides. Motors corrode and the heat exchanger will catch what ever is present. The only other place I know to check for sediment build up is the block drain plugs. Side thought , a collapsing intake hose will give you a fit.

Ok thanks Mobile. I just flush with the mouse ears over the intake holes on the bravos. Nothing as advanced as an inboard connection.