I'm rebuilding my 2.5L (1999 SE, 240k miles). It had a knock that wasn't fixed by changing rod bearings and lifters. Here are two pictures showing passenger side piston scoring and lateral (front to back) piston clearance, which is huge (> 1/32"). I'm hoping this is the source of my problem? The knock was around cylinder 3 as best we could tell using a mechanic's stethoscope. It wasn't there on cold startup and gradually got louder as the engine heated up.
