Before I totally abandon my 2001 project I just want to clarify one thing. A misfire can not cause a rod to rattle can it? I got the engine running again but throwing a misfire code and definitely not running on all cylinders. Has good compression but at idle and low rpm's has what sounds like a rod rattling.

 

Depends on how bad the misfire or timing is. Early timing can cause detonation/pinging which will cause rod knock. Excess buildup of carbon in the combustion chamber can also cause detonation which is a misfire.

 

You can always run another compression test to rule out rod knock. An exhaust leak at the exhaust manifold sounds like valves ticking. You can try seafoaming to see if white smoke leaks out of the gasket area.

 

Typically one way to trace a rod noise is to pull plug wires 1 at a time until the noise goes away. If the cylinder has a dead miss, the rod won't make any noise because the pressure is of of it and it is just along for the ride. Tracing down the missed would be the next step. Now if there is predetonation in a cylinder, that is different altogether. Good luck!