My suspision is you have an exhaust manifold/elbow rerstriction.
Are the exhaust manifolds rectangle in shape? If they are you have a older outdated style, Not very efficient. That bieng said, there are basically three issues regarding high water temps. Incomming water supply, good impeller and no restrictions or air bubbles. Thermostat and housing in good shape (not rotted away). Water exit, if the manifolds or elbows are clogged or restricted they will not allow the hot water to exit the motor fast enough.
As far as replacing the water pump impeller in the outdrive, Did you put the large 1/4 inch square oring on top of the water pump housing? This oring keeps exhaust gasses from entering the incomming water stream.
DId you look up where the copper tube connects? The tube inserts into a rubber "boot" into a plastic diverter in the upper gear housing. Sometimes and I have seen this myself many times, the rubber boot gets pinched by the copper tube and partialy clogs the water stream......May be worth looking at.
Note: the exhaust flappers are there to keep water coming back wards into the exhaust manifolds while in the water. Running on a hose they have NO affect on anything.