yamaha 225 0x66 dropping RPM's

[baked alaska]

I have 109 hours on a pair of 01' 225 saltwater series yamaha's. The motors have been great to date until just after my 100 hour service. At 104 hours i noticed a hollow knocking sound at in-gear idle (600rpm), as if something was loose. It does not knock in neutral, even when increasing RPM in neutral, and the knock goes away when RPM's raised over 1100 while in gear. The knock does not appear to be coming from the lower unit or the motor, i would list it as coming from the very bottom of the motor, even with the cowling off I can't comfortably pin point the location! Sometimes the knock is strong, sometimes very very weak. Could the tube from the water pump to motor come loose at the top of the motor and cause this knock (about 5 knocks per second)? I even took apart the water pump thinking i had impeller problems, but the pump and impeller look brand new, flushing looks good too.
I'm not sure if its related, but I am also losing RPMs after being at 5400 rpms for about 15 to 20 seconds. The motor settles in at about 4700 rpms and the motor feels loaded trying to regain the RPM's. I have the manual and have completed the o2 sensor change (quite a bit of carbon), thermostat change (tested ok but changed anyway), checked PCV sensor, and checked fuel system (checked ok with fuel pressure guage). I switched fuel supply lines and still had the problem. I ordered the test harness to see if i can get any additional info, another yammie owner suggested a bad coil, but plugs look good (only 5 hours on them!) and idle feels relatively smooth (same as good motor). From reading the book, i'm not sure i want to test the coils myself for fear of screwing up the CDI. I did find a baddly corroded and brittle 4 wire connectior in the motor area near the fuse box (pink, orange, black, grey,) those colored wires seem to tie-into everything i checked, but replacement did not improve the issue.
Any thoughts? 2 separate issues or 1 interesting one? Thanks for any advice.

[hooken203]

I had something like that on my 99 Vmax 225 I found that all the bolts that hold the powerhead on to the mid section were loose. If you remove that lower cover that goes around the mid section you can look at these bolts. When I would cross another boat wake it would lose RPM and then slowly pick it back up. The knock sensor was picking up the noise caused by a loose motor.

[baked alaska]

thank! i'll check that this weekend and post the results. Sounds like a good check to do. Your other posts have been very helpful too, the fuel pump diaphram is my next step if the bolts don't do the trick as i suspect flooding as well. Did the bad diaphram present any noise that was noticable?

[baked alaska]

i checked the bolts, a couple were slightly loose. The knocking sound is still present after shifting into gear and staying at idle. Now the oil level light is coming on, even though the remote tank is half full and resevoir on the motor remains full. I'm also starting to wonder if its a throttle cable issue since the motor seems really strong up to 5000rmp. I haven't read that chapter yet! Didn't check the low pressure fuel pumps yet because i didn't have the parts on hand if they were bad. ordering today.

[Island Guy]

I'm reaching on this one but could you have a wrist pin failure on either nos. 5 or 6 cylinders? The way to check and it's a simple one is to remove the plugs (all) bring the no.5 cylinder up to TDC and carefully incert a no.2 philips screwdriver in the plug hole and see if you can discern your knock noise by pushing on the top of the piston and feeling if it "gives". If it does it will make a little noise and their you have it. That would also explain why you can get top rpms and then slowly that rpm comes down. Knock sensor doing its job.