Just shooting from the hip here and maybe barking up the wrong tree....................but if all parameters with the engine check out i.e., oil pressure, power, no misses or hiccups, compression, still pulls out hard etc., I would ask manual or automatic trans? The guys here have a whole lot more experience than me. Maybe if auto, a converter bolt, flex plate bolt, converter after trans fluid heats up? Manual trans, well maybe flywheel bolt, pressure plate bolt or such. Little too much crank thrust clearance??
Does the knocking follow the engine RPM's in park (auto) or neutral (manual)?? A broom stick would reach the trans or general area of the bellhousing from underneath the car. I have used a stethoscope myself and it's an invaluable tool to at least get you in the right neighborhood.
Good luck and stick to it. Not my intention to send you on a wild goose chase.