Did you check the fuel cooler that is between the sea pump and engine oil cooler?

http://www.mercruiserparts.com/bam/s...1374/11743/140

I dont see where this would be located. The Sea Pump hose goes directly to the Oil cooler

Follow the hose out of the bottom of the sea pump, it should go down under the front of the engine, that's where the fuel pump and cooler are hidden

Have you checked this ? Drive and transom changed . Is the 1 1/4 line from transom new as well. Was this issue there before all this took place?

To be honest im not sure where this fresh water flush system is. I have never used it, and im not 100% sure what to be looking for there. The drives are both brand new with maybe 1hr run time on them. The port side had the problem before I had put the new drive on. I figured I would have found it a lot easier, but its been an on going summer killer for me.

I also haven't seen this fuel pump cooler.

At this point some photos are worth a thousand blind guesses, if you can figure how or text to someone who can put them up someone will find the issue for you.

When you cleaned the strainers, was there anything in them?

You replaced the sensor as well as the impeller and the housing, which none fixed it so the problem is most likely a "clog" in the system somewhere, IMO.

Maybe try removing the water line coming from the drive into the sea strainer and put the water hose in it and check to see if the water flow that comes out of the drive is similar on each side....if it is than the problem isnt on that side of the system.

does you setup look anything like this ?....the fuel cooler and the pump is right below the crank pulley

As to late said , if you can't get to the strainer feed line maybe pull the pump feedline and backflush it to check for a restriction.