Welcome, Sam Adams Winter Lager Please..
I run a 2008 16' Waterman with a F40 Here 35 hours and it's had three card jobs. Twice cleaned and the last time replaced. I'm well versed in the problem. Yes it is a fuel problem. You have E10 in your tank? That is the most likely cause.
Here is the scoop I got right from the horses mouth, Yamaha.
1. EFI 40's are not in the market yet... SOON they claim. Last I heard Mid February. But that could have changed. Yamaha claim that the new EFI motors will not be as susceptible to the E10 issue as the carb F40's are.
2. The most likely problem is the idle speed jet is getting clogged. Is you problem bad idle, won't start, bogs when trying to throttle up?
3. From what I have been told the problem is that when E-10 fuel when it sits for a while, as we all know creates all kinds of problems with water separation etc. The idle jets are so small that a residue starts to build and clog them. It get's worse over a short period of time. Much like a pear in a oyster. Once it starts it attracts more particles and builds up a clog.
4. The only way to completely clean the problem is with an ultrasonic cleaner that Yamaha has. Most repair facilities do not have this cleaner as they are about $2500. A typical carb cleaning will NOT do the trick as small particles are still in the idle jets and it clogs quickly after the cleaning.
5. Once your carbs have been properly services or in some cases replaced you HAVE to start a fuel stabilization regiment. A lot of folks claim that - “MARINE” Formula STA-BIL Ethanol Treatment & Performance Improver – Is the best additive to date. This is what we are currently putting in the tank connected to the F40. The key is to use the additives at EVERY fill up.
6. I hear rumors that the Idle jets from a 2001 F40 are larger and might work if they are swapped out. I'm not sure on this and would chalk it up to internet rumor until proven otherwise.
I hope this help. I can honestly say been there done that.
I hope your problem is solved quickly. Welcome again.
Cheers
Capt. Jan