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Old fuel could cause all sorts of problem, if you are sure you have good spark, compression and injector pulse. I would start with getting some fresh fuel in the tank and clear all codes and see if the misfire clears. I would also make sure you do not have any back pressure in the exhaust system. Check these for me and post back and we can work from there.
Well as you know, you need proper fuel pressure, injector pulse, compression and good spark in order for the engine to run correctly . If you are sure you have all of these then did you check the exhaust for any restrictions?
I would have to agree with everything else you have checked, there really is not much else left it could be. That is about the only thing left that makes sense.