Manual fuel pump diaphragms, high pressure electric fuel pump screen, the hidden screens, fuel pressure regulator or the O2 sensor. I hit any problem on a Yamy anymore, I change out the manual diaphragms first thing.

Recently dealt with this on a good friends boat. Being a HPDI it is inevitably one of the fuel filters. Start with changing the regular fuel filter as it is cheap and requires little work. If its not that then the replace the strainer. It will 90% be this but it is more money. THeres a tricky clip on one side of it to get off. PM if you have problems. Still no fix there are 2 "mystery filters" set into the fuel pump that would be the next option to change.

Ok thanks guys I'm going to take it in and a compression check done. And check the computer.

The marine dealership called today told me my boat was ready. They told me that they had to replace the fuel filters and there was some pluggage in my high pressure fuel pump. They said that once they changed everything and they hooked it up to the computer everything was perfect. The total bill was a little less than $800. Ouch!!! I guess its not bad to do all this being as my 5 year warranty runs out on Jan. 14 and I want to make the motor as reliable as it can be for the remainder of its life. I will have to see how it runs when I get back on the water.