I've had my Kohler 5E for the seven years that I've owned this boat - it has be a PITA and a money sink from day one. With the amount of $$$ I've put in over the years I could have paid for a new one - but that's water over the proverbial bridge.
I too have considered going diesel but have been concerned about (1) mixing fuel sources on the boat and (2) where and how to mount the fuel tank. From what I've read the fuel tank is only 13 gallons and if diesel is anything like gas that only provides about 13 hours of running time. With a full load of 350 gallons of gas I do like not having to worry about running out or did I remember to top off the diesel tank.
If I can figure out how to convert my wife from wanting to see the boat go to someone else (she's a non-boater & non boat spender) to agreeing to upgrade the genny, I think I would go with a new 5E with the sound enclosure and try to find some way to protect the genny from the salt water. I think a new 5E with enclosure is about $9k which, when you add the conversion cost to diesel, starts to account for some real money.
Just my 2 cents.