Small Engine Troubleshooting Problems? Ask a Mechanic Now.
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The first thing that comes to mind is if you have an air pocket in the fuel system on the efi it will cause this type or erratic performance. I would suggest that you bleed the fuel line and make certain that there is no air in it. You can do this by using the valve that is in the fuel rail, it is similar to a valve stem and if you push in on it with the key on and the fuel pump operating it should disperse any air out of the lines. If that doesn't solve your performance issue then I would be looking at one of the ignition coils as a potential problem, if may not be firing all the time which will cause the symptoms that you are having.
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A leaking head gasket could cause you to loose power on the one cylinder. It would not gain power back however as you had initially commented. It would affect the O2 sensor and could make the engine run real erratic.
It is possible that the leaking head gasket could be causing the problem.