Thought I'd put my two'penneth in! I have had a Mikuni MX7 in the 90's and an MX60 '95-96. Whilst I never had any problems a lot of my fellow moorers with Mikuni's had endless problems with theirs like you describe. There did not seem to be a common reason for the faults. I wonder if, when one considers that these units (whatever brand) are fitted to road vehicles, the problems do not appear to occur - at least with the same regularity as on narrowboats. Perhaps it is something to do with (1) a lack of ventilation or (2) long continuous periods of use or (3) sometimes dubious fuel quality on the cut. We didn't use ours much and did not have problems. We managed to get by with the magnificent Squirrel stove and cool bathroom and bedroom scenario.
A very well known narrowboat builders in Warwickshire (run by Sam and Dom), have, or had used Webasto units for years and as far as I know they reported the best reliability of the lot........................ I always remember being at a boat show at a well known German branded manufacturers stand, when a very disgruntled boater turned up with a cardboard box containing his diesel unit. He explained to the German representatvie all the problems he had been having. After a short pause the rep said (in complete seriousness) "Vell sir ze problems u are having are not ze fault of our unit zo, it must be your boat". The boater threw the box on the floor and told the rep to put it where the sun doesn't shine (or does in the reps case!!).
Having said all that, our Mikuni although lightly used, performed extremely well. If I were to use one of these things in future, I would ensure I took note of the 3 points above - hope this helps.