[Brian R.]

Sounds like it's time to examine the bottom end and replace bearings as needed (most likely rod bearings). Also, check out your cylinder walls. If they are scored, then you are looking at serious work. Don't drive it any more. May turn out to be easier and cheaper to just replace the engine.

It stopped making the knocking noise when you pulled the plugs because you weren't making the crank/rod bearings take the load of compressing the charge. Once you load them by installing the plugs and making the pistons/rods/crank do work, you hear the out-of-spec clearances caused by the bearing wear.