I am currently having exactly the same trouble with exactly the same furnace. I am suspecting the Flame Sensor only. It requires "rebooting" only when cold - after not running for a few hours. To prove my theory that it is the Flame Sensor, I slightly warm it up with a match befor restarting the ignition cycle on a cold morning. I also have removed the circuit board an resoldered a couple of possible cold appearing connections. I might clean all the varnish off and hit all of them with the iron.
If it is just the Flame Sensor, where can I buy just that? The whole Johnson Controls box with igniter & sensor is too high dollar, unless I absolutely must.