Help with 1989 Yamaha V-6 225

[stratos77]

I have a 1989 Yamaha 225 V-6 Excel. I was on plane running down the lake saturday when I heard a "Clank" come from the motor. I had traveled about 3 miles down the lake at nearly full throttle when I heard the noise. I did not lose power or see any smoke. I immediately shut it down. I was still able to idle forward so the prop could still spin. The motor continued to make a grinding noise every second or two but was not constant. I turned it off and *****ed to the nearest ramp. Got back to camp and took the plugs out to see if I could see any metal shavings or anything. Looked fine to me. Could it be a bearing or some type of gear? I'm assuming (and hoping) that it is not the lower unit since i could still idle forward on the water. I just had a new lower unit (remanufactured) put on in march of 2009.
Any ideas on what it could be??

[99yam40]

drain the lower unit and see what comes out to see if it is inside that.

And then do a compression test if that was not a problem.

I have found pieces of pistons hung up in the through prop exhaust before when the boat operator said he heard a clanking noise, but motor was running fine. But that was a Suzuki