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This sounds very much like a bad thermostat. Have you tried replacing it?
When this happens, are you getting 24 volts AC to the gas valve terminals?
Of course, it could if it's getting insufficient gas. It may not be sufficient to allow the burners to light. Most heaters, water heaters, and furnaces operate on 3.5 inches water column gas pressure and need at least 6-7 inches WC at inlet.
I would not go as low as 5 inches water column at inlet.
But I would still need to know if the gas valve is getting 24 volts on a call for heat. Just because you replaced all the parts does not mean there could be some bad wiring, etc on an old unit like this.
Is this a 24 volt heater or a millivolt system?
Yes, I would try that.
I had asked you a question which I need an answer to in order to proceed. Is this a 24 volt system (power to it) or a millivolt system?
OK, and has the millivolt section been tested? These usually require a 750 millivolt thermopile but there needs to be enough power left over to power the valve.
OK, gonna open this up to other experts. Please do not respond until another expert picks this up.