What if I attach a U joint to the bottom of the JPipe, and have it take the flow up, above the WL to a cylindrical style muffler, then have it dip back down to exit via the outlet. That way, if water were to come surge back in, it'd have to go up, expand in the muffler, fill that, go back down, and back up before it can go into the manifold?
With this setup, I think I'd have to keep the exhaust pipe at or below the highest point of the JPipe, but still above the WL (when not on plane).
For this specifically, I think the JPipe should go directly straight down to the waterbox (a large box that can hold some water but clears out as exhaust passes through, outlet of box is at bottom of box), avoid any chance of long runs from the exhaust manifold which might allow some water to run back into the exhaust manifold and from the water collection box then run up above the water line again, before exiting the transom.
This would provide two high spots, as p-traps and one is the JPipe, to discourage water from running backwards into the exhaust ports, and the 2nd is to discourage seawater from running from the lake and flooding the waterbox.
I think you can closely duplicate the factory exhaust including the waterbox, maybe you have to modify the waterbox slightly due to reorientation, the waterbox outlet must be low in the waterbox so the waterbox doesn't fill with water, only a small volume of water remains in the waterbox while the engine is running, the remainder of the water is carried out of the WB outlet along with the exhaust, up past the 2nd high spot then gravity can do the rest.
Maybe this is what you're thinking:
You could attach the muffler at the JPipe almost vertical, and with the outlet of the muffler pointing down, allowing the muffler to perform the same function as the waterbox (a place of volume for water to collect, instead of running backward into the exhaust manifold), then run a rubber/plastic pipe back up to above the waterline then from there back down through the normal exit.
In this case it's functionally the same aside from the location of sound deadening, the exhaust flow should keep the muffler from filling with water.
Anyway, I think you're on the right track.