Help with new rebuilt motor

I just finished rebuilding my 350 merc new cam manafold and carb. when breaking in the cam i noticed the right exhaust riser and elbow were almost too hot to touch and the left side i could lay my hand on. during tear down i had both exhaust manafolds boild out and re powder coated so there is no rust inside and water flow to each side seams about the same. I am afraid to run the boat in ths condition with the engine cover in place and don't want to burn up a new motor. This one has me stumped any help would be great thanks.

Are the spark plugs all looking about the same? Just want to rule out any possible issues with a lean cylinder or bank of cyl's that could cause excess heat.
If you've already checked the water flow the following may not apply but just remember to check it at higher flow rates because a partial blockage may look fine at idle but won't flow any more at higher rpm and flow rates.
There are block off type manifold to riser gaskets, make sure you don't have one on the hot side (no holes for water to pass thru from the manifold to the elbow.) Many times boiling the manifolds and elbows still won't get all the rust out (the centers of the manifolds usually need to be cleaned with a stiff wire and/or whatever you can get to fit back in it. Try removing the drain plug/s on the manifolds and make sure you get good flow out of them when running the motor. You could hook up a hose to the inlet of the manifold and see how much water you get to run out the exhaust at full flow, and then compare to the other side, just make sure you have the exhaust pointing downwards so no water backs up to the cylinders (tilt the front of the boat up a little.)
Lastly, you can disconnect the water hose at each manifold and see how much flow you have into each side as it could be a problem with distribution from the t-stat housing.
If you can keep your hand on it then it is probably ok as most systems don't flow completely even to both sides. Closed cooling systems that seperate the manifold from the riser (antifreeze and fresh water respectively) will generally let the exhaust run a little hotter to the point of not being able to keep your hand on the exhaust so I wouldn't worry too much as long as motor temps stay good, plugs look fine, and you get some water from each side.
jd

Thanks for the reply I pulled the plugs and they all looked about the same color. I pulled the hoses and ran a wire around in the manafold and felt no rust. water flow out of the exhaust hoses a little different from side to side so off came the thermostat housing and nothing going on in there all looks good. So off to the lake tomorrow and i will try putting it in the water and see what happens. Thanks again for the help

Thanks for the reply I pulled the plugs and they all looked about the same color. I pulled the hoses and ran a wire around in the manafold and felt no rust. water flow out of the exhaust hoses a little different from side to side so off came the thermostat housing and nothing going on in there all looks good. So off to the lake tomorrow and i will try putting it in the water and see what happens. Thanks again for the help
I know at my house we do not have enough city water pressure to run at 2000rpm for any time. You will know when you put it in the water for sure but I know mine will run warm if I run it on the garden hose. Just a thought.