I had the same problem with my 2008 CR. I just picked it back up from getting worked on. My problems were a leaking outdrive seal (not associated with the horsepower problem), the 12v outlets didn't work (they still don't) and I had problems getting on plane and a top speed of around 30 mph.
The horsepower and planing problem was a sparkplug wire that was not connected. It's amazing the difference on gas when you have all cylinders firing... Much better. The engine isn't working as hard.
My suggestion would be to not even mess with it though. Take it to the dealer and let them figure it out. My dealer (Tomes) is about an hour away by boat, along with all the jockeying with cars, but worth it.
Good luck.