How about the back of the rear seat in the engine compartment? If not the transom, it is thick so you shouldn't have to worry about running a screw through. I would also think that if you could mount it under a rear seat, it would make it real easy to plug in without having to lift the engine compartment.
You also stated that you run your Perko on all, but will be charging on either 1 or 2, so mounting it next to your Perko would work good also. You could mount the charging leads to the 1 and 2 lugs on the Perko rather than to the batteries.
Good ideas. I think I am going to look at putting next to the Perko under the rear seat. Hooking it up to that will also help clean up the engine compartment a bit. Thanks for the help/advice.