Was never the engine to begin with, it passed all the litmus tests there.
All the symptoms when the noise was happening pointed away from the engine being the problem according to the OP diagnosis.
Trans in gear, out of gear, clutch in, clutch out ect....
At this point need an experienced tech with a stethoscope up on a lift.
Shouldn't take long to narrow it down to a component.
Ok got the pistons and rods out, looks like piston slap is my problem but not 100% sure. Not sure why its slapping when its already warm and comes on when driving but revving in neutral has no knocking. Still holds good compression 200psi-210psi. Gotta take my block to machine shop to have them check the bores, check the clearance From piston to wall.
Yup. That makes no sense.
Piston slap goes away when the engine is warmed up.
Somebody screwed up clearancing the cylinder bores for those pistons bad if that is truly piston slap.
Bore gauge the cylinders and measure the pistons. Check against CP specs, see how far off they are.