Shoot through the hull should work well, as long as there is no ar trapped between the transducer and the fish you are trying to find, the sonar signal is lost in air.  Use marine goop or epoxy, rough up the inside with sandpaper (to make the goop stick) and stick the ducer in with ease, so not to trap any air under it.  Put a weight on it to hold in place till goop dries, and you should be all set.  As far as the scratches, as long as they are in water, no air should be trapped in them, so no problems! 

If you use a foam base to act as a dam for your transducer, then you can deflate one of those big  xercise balls (or even a beach ball) and then put it in the boat and pump it back up and leave it until it cures. This works especially well on boats that have a V-hull and no real flat spot to mount the base (some people call it a dam). It will mold the base to the shape of the hull and help ensure no air bubble get in. After it cures, deflate the ball, fill the hole with lexel, insert transducer, cover the rest of the way with lexel and let cure, it is ready to fish the next day.

Chad

The "V" doesn't matter; however, make sure that you mount your transducer completely horizontal (to the water surface) otherwise you will have skewed fish arches. You may try making a little dammed area out of modeling clay, fill with your choice of adhesive, then insert the transducer to dry.

Lexel, Goop, construction adhesive, concrete, wattle & daub, it's your choice. All work well provided there is no trapped air bubbles. Color of adhesive is irrelevant; if it were, the color of your kayak would determine the quality of the signal.

You'll never get a completely accurate temperature, but you'll have a good idea if you cover your transducer in the adhesive you use. The heat transfer from water to hull to adhesive to transducer will be more accurate if it's not measuring the temperature of the inside of the boat; hence it is insulated from the hull air by a conductive layer.

Hey Joe - how's New England?