Sounds like you've done all the right things. Two comments.
1. Don't know how the cooling system on your engine is run, but the Universal 5411 on my previous boat would overheat if the thermostat was left out. The thermostat was needed to force water through the engine out the exhaust. Otherwise the water just recirculated and got hotter and hotter. Yours may be different however.
2. You may still have some blockage in the engine passages. Despite use of oxalic acid to clean the engine passages, I found 5 of the 8 plugged when I pulled the head on my previous 5411.