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one riser hotter than the other

I don't know what model you have but there is a raw water bypass in the thermostat hsg. that can close and reduce water flow.
 
I hope he finds the problem, because I am having the same one too. I had not winterized my boat and had to install a new engine. After that, one of the manifolds is cold to touch while idle and the other one you cannot leave your palm on it more than 2 seconds. If I open the throttle with medium load in the boat, the engine sounds like valves are hitting and after about 10 seconds the throttle closes itself. The mechanic replaced the impeller and it did not resolve the issue. Its a 4.3 Merc I/O Vortec with risers and manifolds new.
 
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