Chronic problem with my Yamaha 200 HPDI. The motor occasionally loses top end power almost like it is running on 5 cylinders. It was rebuilt due to a blown power head last year and had similar symptoms before it blew.

The last two one-day fishing trips, it started fine, got on plane fine, but would top out with about 20% less power than usual. Both times I stopped short of my planned destination and fished for about an hour. When I started back up it seemed to run normal the rest of the day - with maybe just a time or two where it sputtered at full throttle for just second which was almost unnoticeable.

I have had all the typical filters, fuel lines, and pump ball replaced. One item excluded from the rebuild last year was the high pressure fuel pump. I have heard there are some filters in the high pressure pump also that are difficult or maybe impossible to replace. Any thoughts here?

I would have all of the injectors serviced plus the hidden filters soon before you blow it again:

Pardon my ignorance, but what is that a picture of?

Hidden fuel filters

It that a high pressure pump that the filters are hidden in?

Yes

Chris have you pulled your pump and replaced them ?? I have never done it, Lance at F&S may have at some point.. I change out all the one's I can get to regularly, and I added a water seperator w 20 bizillion micron filter. Hopefully I can catch any bad stuff before it gets that far, been ok for 13 yrs..
To the OP,
I had some old/ bad gas cause mine to stumble on higher rpm's, it didn't take long to go bad.. Chuck at service marine said it lose's octane power quickly, he gave me a pump to sux it all out, and into my truck. Ran fine in the truck's hemi.. Justsay'n
New plugs, and fresh gas, boat runs like a scalded dog...

Thanks, yes I have a large gas tank and tend to only add about once a month. Maybe I should start running it closer.