I'm putting this thing back together and will start it soon. I found that one of these small head plugs had rotted through and was told by the local machine shop that this will cause an exhaust leak sound. I'll know for sure when I start this thing in a few days here.

 My sons jet boat had a rock the size of a golf ball stuck in one of the bowl veins. Surprisingly the impeller didn't look that bad for having a large rock pass through it. If you pull the bowl off you might find something going on there. 
 

 Pics

  Did you ever confirm what was making your noise?

 I'm not saying it's not an exhaust leak, but when looking at the manifolds and heads, I don't see any carbon areas that make a clear exit out of the contact surfaces. When I pulled the heads the gaskets tore apart, preventing me from seeing any type of leak that could be coming from them.
  I'm probably going to just clean everything up and put new gaskets on and run it.

I disconnected the belt but still had the noise.

  Push rods look straight, rocker assemblies all look perfect, The lifters can all be pressed in little with a push rod except for the last one on the drivers side, intake valve for #8. That's the same cylinder that has a black plug all the time. I took it apart and removed some oil. Now it moves in and out like the rest. Can a pumped up lifter make a ticking noise? I don't see any contact with valve to piston.
  I'm really wondering if my head gasket was leaking between #7 and #8. These are some pics.
  Oil pump seems smooth also.

Pulled the motor and the rod bearings look like new. None are spun. The heads are lifted and pictured over their cylinders in the pics. The rear drivers cylinder, #8, always had a black sooty plug. You can see the exhaust valves to the rear of the motor look to be running richer than the rest. Not sure why. I'm wondering if the head gasket was blown in a way to give an exhaust leak internally? Can I bench test the lifters?

 That's the insulator that is between the wear ring and the pump. Where's the wear ring?

Is this a rebuild? New head gaskets? Might not be the right ones or on wrong?

I've got one of those mechanic stethoscopes and placed it on the fuel pump when running and didn't notice anything but I do have a spare to try. I'm going to try pulling plug wires one at a time and see if I can narrow it down to a certain cylinder. It might be an exhaust leak on the bottom side of the logs. No gaskets, just silicone.

  Pulled the oil filter apart and can see some small glitter in the bottom of the sheet metal cover that the oil filter sits in. Nothing noticeable in the filter element. Does the small amount of material in the bottom consistent with a spun bearing?