I have a 5000 btu home a/c unit (small box), and it works ok. I tried it next to the mast, w/ poptop up, and under the canvas cover. worked ok at night, fair to poor during day time (august in fla). I also added a large towel to close off the front (at sink) to reduce size.
better was in the companion way, poptop down. I've seen some very nice boxes built so you could step on the ac units.... I just cut a new hatch board.
What I did was cut a 3/4" plywood base, and tied rope around the the ac thru the board so I could slide it about, and be able to tie additioinal ropes to the a/c unit to secure it to the boat.
however it does leak water into the cockpit. over time it will form rust trails... but I don't use it that much.
before I mounted the a/c to the board I took the a/c cover off, and tied additional wires to the compressor and added some chicken wire to the back condenser to make is more rugged and armored.
I'd say the companion way is best way to go, and build a box that you can stand on.
and they make smaller units now than when I got mine... very small. so unless you have a dock box to put the koolaire unit in, I'd get the home type ac.
OR, you can consider the stand up 7000-9000btu units with the exaust hose... thats even better! but it needs to find a home inside the cabin, and then you run the hose to an small outlet in the hatch, or cut a window.
just get the type that evaporates the water into the hot air exaust.
the koolair hatch type are ok, but hard to store aboard, and pricy. so you'd need to take it back to the car, or put it in a dock box...
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What is you plan for use? marina? extended trip? how many aboard? etc...
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