I don't have experience in your situation as I don't have an I/O, but if you've got rust flakes in you cooling system I'm guessing it's from the manifolds. They would appear to be rusting from the inside out.
All those little flakes are getting circulated thru your system and can glog up you cooling passages.
You said the boat had been in a salt-water environment, but how sure are you that the PO really took good care of the engine maintenance?
I'm not trying to scare and like I said I don't have that situation on my boat, but if it were me, I'd change stuff now.
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1999 180 Horizon OB Fisherman Pkg
San Antonio, TX
Choice of tow vehicle:
'93 Explorer 4x4 (sold)
'05 Grand Cherokee 4x4 w/ 5.7 Hemi (member of the 240k+ mile club!)