If after fully examining the manifold and riser sea water "transfer ports", and after you see no apparent tell tale signs......., look at the division of the spent cooling water that leaves the Heat Exchanger..... or if raw water cooled, the water path from the engine.
Somewhere in your system there will be some type of splitter (or dividing mechanism), that is suppose to split the spent sea water equally between both exhaust manifolds.
If this is not dividing correctly, all else may appear to be OK, but you will have the uneven temperatures that you are seeing.
If closed system cooled, often this is a copper T splitter fitting.
Or.... the Heat Exchanger itself may split the spent sea water via dual sea water outlets.
If raw water cooled, you may have a T stat housing that splits the sea water.
If so, check to see if something is restricting the flow to the side that is warmer.
Whatever you do, try to NOT add restriction to the cooler side in hopes of increasing flow to the warmer side!
Instead find out what's restricting the side that is running warmer.
How about posting a few photos of your cooling system for us?????