Luke,
I'm not sure about the align boring. I bought the short block from an Atlanta engine retailer. The only thing I can say for sure is that the noise is definitely coming from the front timing cover area (which, of course, is where the gears are located).
Yes the thrust plate screws were installed securely, so that's not an issue.
You know what? I didn't even think about "air" in the system. That might explain the "hissing" sound we heard each time the engine was shut down. How do you remove the "air" from the system? Should the engine be turned over several times with the plugs out?
