On my '83 Kingfish with twin I/Os originally there were the two pipes you describe going through the bulkhead between my Fuel tank area and the engine compartment. In the engine compartment end the two pipes had transom type plugs in them to seal them, preventing the water from draining into the motor box compartment. Don't know what your "bilge pump" area is constructed like but can you see the aft ends of the two pipes? If so are there plugs in them? The plugs in mine were the brass style with a "T" fitting that when turned would expand or contact the diameter of the rubber body of the plug. My guess that is what may well be plugging your pipes. I could never figure out why the plugs were in there unless they were worried about a fuel tank leak passing fuel into the engine compartment but the one from the forward bilge was plugged also. When I repowered the yard removed the pipe from the fuel tank area into the engine box and just fiber glassed a hole in the bulkhead so it could not be sealed with a plug. Hope this helps. Keep that old Grady going!