Just went through this with our local Yanmar distributor. First he says a lot of people have soot on their transoms because he is always being asked how to clean it, so not to worry about a little bit. Second, warm the engine up, and see if you can get max rated rpms in flat water. If not, you are probably over propped and that is what is causing the unburned fuel. Dirty bottom and/or fouled prop can also be a cause. But If you can reach max rpm, then you have been running the engine at too low of rpm for too long. Run the engine at max rpm for about 30 minutes. After 30 minutes, start at idle and hit the throttle pretty hard a few times. He said this would seat the injectors and clean them out a bit. Then be sure to always cruise at a minimum 80% of max rpm. A little higher won't hurt.
My Yanmar has a max rating of 3600 rpm and I have been cruising at 2800. I following the above procedure, and then have been cruising at about 3000 rpm all summer, and we motor a lot here in Puget Sound country because of summer light and flukey winds.
Just a slight trace of soot on the transom after 67 hours.