Why does my heater have a weak flame after restarting?
The thermostat should turn the system on and off. If you are having problems with intermittent flame you may have moisture in your line. I usually install drip legs after the shutoff valve prior to the furnace, water heater or range this traps the water. A drip leg is a T with a short section of pipe going straight down that is capped. This leg catches rust, and moisture. 1 drop of water in a gas valve can cause problems so I would check to see if you have a drip leg and if so shut the gas off and clean it. If you don't install one. I have had homes that had horrible moisture problems in gas lines and others that had almost no problems. Since you have thrown all those parts at it I would be looking at moisture as the possible cause.