You do not need to buy a new separation cover plate.
It will be deformed too as the heat from the exhaust will make it to warp.
use the one you have.
Check if there is some leakage at the covers or damage.
You need new gaskets and yes pull the head too and check the head gasket.
BTW Another possibility of water intrusion in the bottom cylinder is a bad crank seal at the end of the crank shaft.
I already got the plate for 75 shipped, no biggie. I actually had to re-surface the exhaust cover, it was warped 0.020 which is bad. I used the sharpening stone in the picture and it is now at 0.002. That is acceptable. The crank seal at the bottom was replaced when I rebuilt the damn thing. I had the crankshaft out in pieces. Every seal on this engine is new.
The exhaust cover was way too warped was wondering why every time I torqued the bolts they were loose again in a few days. I will now brush some liquid gasket maker 500C on all the surfaces and use the recommended 750 industrial sealant on the bolts. I truely hope it is the end of the ordeal. I mean there is no part of this motor I haven't touched.
I am just sorry I didn't check the cover and use a straight edge to check the warping. It is weird that the boat was able to ride at all. But the water obviously affected the running at idle in gear. I guess water doesn't light up like gasoline and oil hahaha. I sure hope there is no other reason for the leak as you mentioned. Fingers crossed.