Interesting Decision
We bought our boat in '94. I had no prior experience with owning a marine diesel. So I called Universal Westerbeke and spoke with an engineer about maint. and life expectancy and he told me not to worry... that as long as I kept clean oil in it and generally looked after it it should go at least 4500 hours before anything major was very likely. And it might go on a lot longer than that.
Pretty similar advice from a local diesel mechanic that I know, too.
I had just under 1000 hrs on it then and is close to 2000 hours now. We change oil every year and never have to add oil. It starts quickly and does not smoke.
One point that our mechanic friend makes to
all sailboat owners (and to most trawler owners as well) is that "light use" is a lot harder on engines than running for hours at full load.
Given that you say you have used yours only to get in and out of the marina and now have 5000 hours on it.... it sounds to me like you have a better-than-average engine. I might lean towards installing a new engine/trans/panel with a nice lovely new warranty if anything major hiccuped on an engine with those hours on it. After all, it isn't just the reliable Kubota engine short block to consider, but all the spendy marinization parts on it that get old/worn/thin as well. Of course untested opinions are cheap. At crunch time I might opt for the rebuild, too. Here I am, speculating about the scenery down a road I have not yet traveled...
FWIW, I am hearing very good things about the newest Kubota blocks regarding both economy and cylinder head design. What that's worth, if anything, for an upgrading and older sailboat is extremely subjective.
Best,
LB