Did you check your compression with throttle wide open and at operating temperature? With all plugs out and fuel discharged? Lack of compression in CYL 3 could suggest a connecting rod bearing letting loose creating lower compression numbers compared to other cylinders.
~Now that you verified compression is within spec keep in mind the elevation you are at, do a leak-down test and see what happens.
I did have an EJ25D make a similar noise however it was more consistent through the rev range ~Turned out someone timed it a few teeth out.
Just start basic and do all the standard diagnosing procedures.
-Leak-down on all cylinders
Just my two cents