Vinegar was my first thought when I read rust.
I think I would pull the thermastat, reconnect the housing, drain as much water out as possible, and fill it with vinegar.
Start it up and let it run for 3 minutes, then shut it off and leave it overnight.
Next day, drain and flush with water, install a new thermastat, and see if there is any improvement.
I soaked some chains that were rusted solid and it made them useable again.
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