Engine cut off at 3000RPM

[lateralinfo]

one of my engines starts cutting off at 3000RPM after some run time (around 30 minutes or so). the weird thing is, if i shut it down for a minute, it goes back to normal before starting to cut off again.
to give you a bit of history, this engine has had a "water in fuel" alarm less than a year ago. immediately, the water separator was replaced and the engine's fuel filter was cleaned. it was back to normal since then.
to try and narrow down the search for the faulty part, we exchanged the fuel pumps between both engines. now the other engine is acting out. so it must be something to do with the fuel pump.
the dealer is suggesting replacing the fuel pump altogether. but i am trying to see if there is a "cheaper" way of fixing this problem. so my questions are:
1- what is the harm to the engine if i keep it running like this and whenever it starts cutting off, i turn it off for a minute and then start again? any risks? just a temporary fix for the moment until the diving season is over.
2- could it be the filter or something other than the fuel pump that is damaged? any experience with a similar case?
3- is the fuel pump repairable or will it need to be replaced?
FYI, i run twin engines suzuki DF300 mod 2017

[RockCanyon]

Not sure how much i can help but a few additional things come to mind-
1. Any time your engine isn't running right, it can shorten the life of the engine or other components. If its cutting out because its starving fuel above 3000 rpm, thats not a good situation. Running lean can damage pistons and cylinders.

2. When you're saying 'fuel pump', are you referring to the low pressure pump or the high pressure "injector" pump (inside the vapor separator)? I'll look at a 300 again to see its setup, but there are quite a few filters by the time fuel gets from the tank to the engine. Had a Df70 with a NASTY gas tank, it clogged the main fuel/water filter, the filter before and after the high-pressure pump, and ruined the pump element.

3. If you have your dealer replace the part, you could ask for the old one back.
then you can play with servicing it yourself if you feel inclined.

4. My take is that you're right, it does sound like when you let it sit for 30 minutes, the pump is able to fill the vapor separator, but at full speed, it can't keep up. Just a theory.
interested to see what it ends up.

[lateralinfo]

i am talking about low poressure, the unit with the water filter and micro particle filter attached to it (sorry, not too much mechanical savvy).

[RockCanyon]

I'm not sure how reasonable your dealer is, but it sounds like you have it pretty well narrowed down already, with the electric fuel pump, they can run an actuator test and see if it's the pump element that's not running quite right. You may be able to get away with replacing just the pump element (if the dealer will allow). Or you can replace the whole unit, since it seemed like the common denominator. I know it sucks, but especially with a high dollar/high hp engine, why take a chance? Also i believe the water separating filter is recommended to be replaced every 400 hours or so. I drain it every oil change, or after the the boat has been sitting for a bit to inspect the fuel.