[tempfixit]

I assume you did not have the valve covers off when the plenium was off. I still think it has something to do with the valve train, broken push rod or rocker arm loose and tapping against the valve cover creating the noise. Only way to find out is remove valve covers and look.

Take a look at your camshaft sensor and syncronizer and see what condition they are in, before getting parts. Same with crankshaft sensor.