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Yanmar's are know to put out some smoke, we have a 3GM30 and it does smoke a little. We have the same thing happen when we have a dirty hull or prop and the engine has to do some extra work.
Also, you need to run it close to full throtle for quite some time. Maybe you have soot build up in the mixing elbow. After running it hard for a while, the engine will run very clean for a long time.
I don't think you have an issue. Diesels build up a lot of soot and since we barely used them in sailboats, it can become a issue. Just run it up nicely, exercise it and enjoy it. Quite a nice engine you have there.
1982 Gib'Sea 105
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