False alarm?

[Mac3]

2 years ago I bought my new boat which has a 98 Johnson 150 ficht. Up until 6 months ago it has performed flawlessly. With iboats help I have since learned a lot about Johnson 150s and am confident of attacking any problem and performing routine annual service. To sum up I have had 2 faults develop together- water in fuel and an internal blockage in the water system, and it took a while to realise 2 things were happening. After lots of retrys I've finally sorted the water problem. With the water in fuel I eventually drained the tank and have replaced both internal and external fuel filters 3 times. I am convinced there is no water in the fuel. While sorting the water blockage the check engine light came up regularly- checking the codes it was the good ol water in fuel. I eventually disconnected the wire from the sensor because 1) I don't think its a problem any longer and 2) if a check engine warning comes up for something else I don't want it to be hidden. Anyway today with the wire disconnected I momentarily got the water in fuel alarm. Apart from the ECU which I find hard to believe, any ideas?? I read elsewhere on this forum guys have had the check engine light on for months and aren't too fussed, don't reckon I could do that!
cheers
David