I took the lower leg of my mariner 75 and stuffed a short piece of hose over the eater tube (that normally connects to the pump output). I then used a sump pump to run a mixture of malt vinegar and water through the engine, catching all of the water in a big bucket/trug to allow it to re-circulate. It ran for several hours and took a lot of crap out of the engine. The only down side was a severe craving for chips.
If you test the thermostat, do it by putting it in cold water and gently adding hot. I'm told dropping it on very hot water can damage them. New ones are pretty cheap though, so probably worth replacing periodically.