Check the pony air cleaner bowl too
The pony doesn’t have an air cleaner, just straight pipe with a twist lock cap.
The plug shouldn't leak anything if it is tight. If you can't stop water getting in the cylinder then think about removing the head and checking for cracks, un-level head/block etc. Go from there. Also consider bad manifold gasket/rust damage.
It is suspicious that this occurred during the storm. Doesn't the pony exhaust exit the side of the diesel intake just behind the air cleaner. With torrential rainfall coming sideways, couldn't this have all started with blown in rainfall?
Now, if I am understanding you correctly, you have an obvious leak around the plugs. Sounds like you need some new heads and head gaskets. They have to be cracked if water is coming out around the sparkplug threads. I suppose you might try some high temp pipe thread sealant or antiseize compound and see if that might take care of it.
I would figure out a way to pressurize the cooling system to 10 pounds or so and remove sparkpkugs to inspect for the source of leakage. I suppose its possible a new head gasket might do it. Its not much trouble to remove the pony heads and the copper gaskets can usually be reused as is or certainly after spraying a thin coat of copper coat aerosol or similar product.
well fellas, I haven’t drained anymore water out of either side so I think I can rule out a head gasket issue or cracked block. I think there is a crack/ hole somewhere in/ on the intake manifoldthat let the water in. The leaking spark plug seems to be coming from some chewed up threads. Think I’ll try a thread sealer. I have a spare manifold so I’m going to change them out.