Intermitant Fault with mag 350 MPI

[gentlemanglobetrotter]

Hi & Help, bought 1st boat couple of months ago, Maxum 2700SCR (2003) only 60 hrs on engine, been fun up to a few weeks ago, now 74 hrs on engine

Problems-
1) Notice leaving marina at idle engine missed a beat every now and again, put on plane @ 3500 revs and seemed fine, out for a hour or so returning on plane felt it miss again, came into marina and ticked over fine
2) Went out from marina and the odd miss again, just onto plane @ 4000 revs when dies, heavy smell of fuel, tried to start would occasionally fire but then splutter to a halt, towed home, back at marina fired up and ran for 15 mins at idle no problem
3) Replaced fuel/water separator filter, on draining fuel from old filter it was very dirty – no water, changed inline fuel filter as well and again really dirty from inlet side, took boat out and tested for an hour ok at all revs, thought problem fixed
3) Went out for weekend, no issues at 1000-2000 revs to destination, stayed the night, next day headed for supplies, all well for 30 mins while waiting to dock spluttered to a halt again, wouldn’t start, 1 hour later got started, running really rough, using high revs to keep running sounded like missing on a few cylinders starting and stopping then all ok, limped back to destination between 700-1000 revs never missed a beat, fired up a couple of time during the night all well, fired up in morning for 30 mins before heading home again all well, loaded up kicked in reverse and spluttered to a halt, tried over an hour to start, would occasionally start but splutter and die, towed home again
4) After being towed back tried to start at marina and wouldn’t so hey hopefully find the problem now, an engineer looked at it and she still would not start, he checked fuel pressure - ok, removed plugs pretty dirty so cleaned and re-gapped - engine now fires up but would shut down after anything from 30 seconds to 2-3 minutes, purring away then just shut off as if you switched the key off, then he phoned back to say engine now running for last 15 mins and not shutting off- arghhh
5) Decided to get Mercruiser dealer to run diagnostic test, he did with no fault codes or issues, he checked the fuel pick up wasn’t blocked says engine running away with no faults and seems to be fine, thinks sea trials required to find fault or breakdown again etc
6) Was down last night, ran engine myself for 20 mins revving etc and purring away nicely – so frustrating

Sorry for the long story but I have lost all faith in her and had the embarrassment to be towed in twice now from the same park rangers, there is clearly something not right and I guess the more information the better so any ideas guys??