I'm finally out of my element...not really sure what to check. It appears the slots are where the water from the cooler rises outside of the center exhaust. If so, then that bad area of the gasket would allow the water from the slot to leak into the "dry" exhaust area of the manifold...and therebye into the lowest cylinders. So it seems to me you may have found the route the water took.
Hopefully someone that understands risers will chime in.