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I have a 2001 Yamaha 150 HPDI on my Jones Brothers Cape Fisherman 1910LT that just this week started to cut out for 1-2 seconds when the boat hits a wave and then will kick back up to running PRM's again until the next wave. Motor starts fine, idles fine, and runs fine until a good sized wave is hit at speed.
Local marine mechanic diagnosed a bad fuel pump which is going to cost well north of $1K to fix (ouch!) and I am looking for second / third opinions on what could be causing this.
Only other piece of information I can offer is that recenty the priming bulb does not want to get hard when priming the motor. I will squeeze it a bunch of times and it will get close to primed and then it seems to just lose its prime and go soft again.
You should look at getting a repair kit for that fuel pump..with the bulb not staying hard seems like the diaphram has a pinhole. What I can't relate too is the loss of power going over waves. Seems more like a loose electrical than a fuel issue...
The primer bulb is only used to fill the VST. If the engine has not been sitting for a long period of time or been run out of fuel priming may not be necessary. Fuel filter service on these engines is critical. It is possible for debris in the filter to plug the filter when you hit a wave. Ground connections any where in the engine electrical system can also cause the problem. The engine runs by switching ground signals, so a loose or corroded ground could cause this problem. carefully inspect all the connections on the engine and the key switch. High tech engines like the HPDI require more trouble shooting skill than older carb engines did.
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I had a similar problem with a VST filter starving the boat for fuel in rough seas, the engine would completely die when coming off of a large wave and then would power right up again, maybe 2 seconds total. Replaced the VST filter and problem solved
I as well had a similar issue with my 200HP HPDI's several times and the problem was with the silver canned filter on the port side of the engine as well as a smaller filter in the fuel reservour.
The silver filter is about $75 and the filter in the reservour is $35. To change these it takes about 1.5 hours.
Had same type of problem with 150 hpdi's . RPM's would drop when hitting a wave. Changed both vst filter and stainless filter right before pump and problem solved. Very easy to do when changing vst filter you might have to change gasket also because it can be a Pain in the #$# getting the old one back. Go on SIMS website and you can find out how to change the filter with photo step by step.
Good Luck
Also there are low pressure fuel pumps that are recommended to be
changed after some time also a very easy do it yourself fix and not expensive. How did they diagnose the fuel pump? was it an assumption?
use a little grease in the slot and press the gasket back in when putting back the top and bottom of the vst canisters,,, little secret,, dont gook it up.. just a slime in the groove. works evry time.. and carb cleaner and an easy touch will clean the vst filter.. Heres, the kicker,, if you have a racor after your fuel tank Water seperator, change it to 2 micron, the strainer above the vst is 2 microns and why in the world would you want that 80 dollar filter to clog when you can clog a racor spin on for 18 bucks with very easy access? I have (knocking wood) not had any more problems now for 350 gallons of fuel since i changed to 2 micron spin on water seperators... any questions,,, just ask,, joe
The 2 micron water separator/ fuel filter is the way to go. Yahamas hate ethanol mixed fuel. I have also seen HPDI's with engine wire harness faults that will act up in the same way.
Yamaha 150 HPDI Cutting out when boat hits waves 
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