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I would remove both lines going to the water heater and blow thru it. It should not take much pressure to get thru (try both directions - blow thru each hose). You could also try an air compressor to see if something dislodges.
Is your engine raw water or fresh water cooled?
I'm assuming if you have a water heater bypass, it is now turned correctly? If you get hot water using electric, then it has to be.
Dream 'Inn III -- 2008 400 Express
2001 310 Fiesta Vee
T-5.0 FWC Mercs w/ B2