I have looked hard, and it is real odd. Water in all cylinders?!?!? The heads are LA heads, and the manifold looks to fit the LA properly. Also, a hole in the timing cover will put water in the crankcase, and not into the cylinders. I see the cork end pieces, but that would only send water into the crankcase, not the cylinders. There is also no way I can see any water getting into ALL cylinders, if any at all. It does look like you used silicone on the end rails on the new manifold, so that again when you put it back. The cork will usually hold up the manifold, and water leaks into the crankcase. The only thing I can imagine is that maybe the heads were not tight. Taking off heads can get water in cylinders, but certainly NOT all of them, and sure as hell not that much water. How hard was it to remove the head bolts?
You are going to have to remover the motor, and have the rods checked for damage due to the hydro-locking. You usually can't see it easily with the naked eye, but we machine shops have an alignment fixture to check them. If you want to bring the motor down here, I can rebuild it for you. You wouldn't be the first from Phx, or from another state even.