Okay, I'm having a difficult time understanding what you have done, so let's start from the top.
Are you running in fresh water or salt water?
Have you dropped the lower end and inspected the water pump impeller? I know you are heating up on the starboard side, but what temperature reading are you getting on the port side? It is possible that the port side is heating up, also, but not enough to trip the alarm. Normal operating temperature is 160 F.
When you took this heat reading were you in the water or out of the water using a test tank or muffs? If the latter, was it a test tank or muffs? If you were using muffs, or a SMALL test tank, that reading is unreliable. You need to take the heat reading either while the boat and motor are in the water or in a large test tank.
It sounds like you are testing the water passages beyond the water hose that comes off the t-stat, is that correct? It would seem unusual to have a blockage where the manifold goes into the lower housing - I don't think there are any narrow passages after the manifold.
If there is a blockage (as opposed to a faulty water pump), then it is more likely around the cylinder walls in the block - that's why you need to back flush from the t-stat opening - down in the section where the t-stat sits in its housing - that is where the water flow is coming out of the block. It is best to do that with the lower unit out and the water pump out.
You said you removed the head gasket? Are you sure you removed the cylinder head gasket - that's one heck of a job. Or are you talking about the manifold gasket?