Sounds like the valves are set right and compression verifies it. This back fire happens after it dies or you shut it down or does it just start running bad and backfiring all of a sudden ? It's possible the flywheel key got sheered and threw off your ignition timing , never saw one run with even a slightly sheered key but you never know.
This may be totally unrelated to your original problem as well ,
Backfiring through the muffer indicates unburnt fuel in my opinion .
Thank you for the reply. The plot thickens. It backfires intermittently when running and appears to be the cylinder with the new head. The other cylinder never appeared to have a problem. Remember I received this tractor running but I have no history. A wire going to the brake safety interlock was pinched under the battery so the mower shut off then the PTO was turned on. Engine appeared to run find after I found the pinched wire. When I received it I did not know it was only running on one cylinder, cleaned it and put it in storage.
I rechecked the valve clearance and they are correct. The new cylinder head had the valve and valve springs pre installed so I did not lap the valves? Should I have done so? My You Tube research takes me to three possibilities.
First, a burnt exhaust valve. It is a new head and valves and has only run maybe five minutes, one minute at a time during trouble shooting.
Too soon to burn a valve?
Second, is the cylinder running lean? I have never worked on a two cylinder before.
Can one cylinder run lean but not the other? The exhaust pipe very quickly turned red!! I have just removed the carb and getting ready to clean it. Note, when I got the tractor I could tell the carb was removed before because the choke linkage was installed incorrectly.
Three, the timing is off because the key may have been moved slightly. Have not addressed this yet, only put penetrating oil on the fly wheel bolt at this time.
Looking for the needle in the haystack!!