Your going to need to use a pump to extract the concentrated brine from the unit, and flush it overboard
before it turns into a solid. This will have to be monitored, and set to a point where the scale doesn't form an insulator around the heat exchangers in the unit. The brine that is drawn off of the unit is as hot as the unit is, and there has to be sigificant heat exchangers to try to concerve that energy. Typical distilation plants adapt to this by using multipul chambers with steadly reducing tempretures, and pressures. They also use recovery heat exchangers to help keep the heat loss to a minumum.
This however isn't your primary problem. Around 150F, sea water will start to form a scale that will deposit on any solid surface. This scale is a sigificant insulator. This is why the heat exchangers for marine
engines are set to remain cooler than that. It's difficult to maintain enough of a vacuum to keep the boiling point of the water below 150F. (Actualy, right now I can't even recall
if that's possible. It's certainly possible with freash water, but I don't recall
how high a precentage you can go with a brine before it's a problem. I really don't want to pull out my old steam tables right now.) And the great thing is that the scale is a great insulator, so the more the scale builds up, the less heat transfer you get.
Also, since we're talking about a vacuum distilation unit, your probably going to be planning to use the condensor to maintain the vacuum. From a theoretical stand point this is great. However, from a practical stand point there are several problems with this. In order to keep the water boiling, the vacuum must be maintained. Any sort of air leak will slowly decrease the vacuum in the unit untill the boiling stops. Also, water as air disolved in it. When you pull a vacuum on the water, some of that air will come out of solution, again, ruining your vacuum. As such, you'll basily need a constantly running vacuum pump to keep the air from ruining the whole system.
I'd like to add that your also going to have a sooting issue from the engine. Diesel engines make soot, and it will tend to collect on things that have cool tempretures, like your heat exchangers in the exaust. The more that soot collects on the exchangers, the higher the back pressure, and the less heat is drawn into the unit.
Not to mention, even the best insulated unit of this size is going to lose a sigificant amount of heat.
As you can see, each of these problems is solveable, but requires weight, engineering, and control. These problems are easier to solve, the bigger the scale of the unit. As a result, most of the avalible distilation units are rather large sized, in order to use the economics of scale in their favor. For such a small unit, using such a small source of waste heat, you've got issues as all of the issues with the scale of the unit work aginst you.