I have a '00 Subaru Outback that I installed a rebuilt EJ25 2.5L long block that makes the same noise. I guess the hydraulic timing belt tensioner can be the culprit. Unfortunately, this is my only vehicle now, so an engine tear down inspection is not much of an option. The rebuild has 25,000 miles on it and it started to make the "knocking" sound after 12,000 miles.....just past the rebuild warranty period. The sound drives me nuts. The engine runs fine, no CEL, and the fuel economy is 15 mpg city, 32 mpg highway. Still driving it sounding like a ticking time bomb. Please post your cure...if you find it. Good Luck!