I recently had the powerhead on my 2004 225 HPDI replaced and thereafter noticed a knocking noise when I put it in gear, only at idle speed. I asked the dealer to look into this; they said it was in the lower unit and since they did not work on the lower unit it wasn't their issue to resolve. This dealer took 6 weeks to replace my powerhead, couldn't send an engine download to Yamaha and didn't know how to order parts on-line. Regardless, I'm fed up with them.
I've ocassionally looked at this site to see if anyone else has had a similar problem with the knocking sound. I recently saw that another guy did and one suggestion was that his idle speed was too low. The rotation of the prop was getting ahead of the flywheel. The fix was upping the idle speed. I was thinking that my idle seemed low and am not getting much of a water stream from the new water pump.

Has anyone else heard of this and is upping the idle speed something I could do.