2001 Ford Focus Engine Knocks, Runs Rough

I recently installed a rebuilt engine in my 2001 Ford Focus (2.0L, SPI) and it ran fine for the first 500 miles, then slowly developed a knocking sound in the engine. I initally suspected the knock sensor had gone bad (98,000 miles on previous engine) and replaced it, but found no relief. I performed a compression test and all cylinders were 150psi (+/- 5 psi) which leads me to believe the piston assemblies are intact. While I had the spark plugs out I cranked the engine over and alas, the knocking had disappeared (it will knock with the plugs in, but plug wires disconnected). This leads me to believe I might have a bad head gasket, but I would appreciate your input before I pull the head off.

Thanks, Joe