As this thread continues I am sure inferances that the problem is really simple and anyone else could fix it fairly easily must be very irritating.
I have two commercial boats as well as my Amel and all have engines with mechanical fuel pumps because this is exactly the sort of problem electronic engines have in the marine environment... when you have a fault it's so hard to know if it's mechanical, electrical or even just software. I'm sure anyone who has experience with engines where a confident diagnosis of the problem is missing will sympathise with Jamie.
My understanding is the initial problem was diagnosed (after the engine was running fine) as the fuel pump not pressurising and the pump and ECU were changed and didn't fix it, and no error codes were found. The subsequent problem discovered was corrosion in the inlet manifold.
If Jamie can bear it, removing the head to see if there is any cylinder or valve damage associated with the corrosion in the inlet mainfold is worthwhile as the inside of the engine may well be fine. But this mainly relates to the second pronblem. Not knowing the whole picture I suspect he still has an underlying undiagnosed fuel issue, either relating to one of the changed parts being faulty or something wierd happening with a sensor affecting the electronic fuel pump management. Another possibility is something in the fuel system but we would have to assume that's the first thing the mechanics checked. I would also check the fuel return as well as supply as I wonder if a blocked fuel return pipe would directly or indirectly effect the pressure sensor in the pump. Probably unlikely but easy to check and often overlooked.
As an Amel owner, having a mechanic critisize the installation, in this case the exhaust system, raises alarm bells. As far as I know that's nearly always is a red herring resulting in a mechanic getting more work before eventually the logic of Amel is realised.
So far this very long thread has still not answered his problem. I think the main use is to help balance the tendency of modern mechanics to too readily change things rather than fix them to save time and effort and make the money from the sale, but I guess Jamie knew that already. It certainly has given him food for thought. Hopefully it hasn't produced wild goose chases and will make him think carefully before redesigning the exhaust system and potentially devaluing his boat.
If I was him, and was that pissed-ff with the engine and was thinking of changing it, I would take it out and get the whole thing to a workshop to get them to try to fix it IN the workshop. I would still probably check the cylinder head first to confirm there was no expensive water related repairs required. If I still wanted to change the engine after seeing the cylinders and valves, and was going on the World ARC, I would probably buy the same engine again to save the very significant hidden costs and compexity of installing a different brand, sell the old block and keep as many spares as I could carry like water pump, starter motor, alternator, hoses, etc. But I'm not Jamie and haven't seen his boat.
John Maruma #91 Popeye