Yes, you will need to cut the cabin sides down to get them to fit properly. When you have the foredeck in place and the notches in place, the cabin sides will probably overlap the transom slightly. You will need to trim to get them to fit properly. On mine, the distance from the rear of the cockpit to the transom measures 9.5", however this measurement is to the inside of the cockpit at the transom. In other words, with the inside trim in place. The measurement from the trim to the hull at the transom is another .25" or so, or whatever the plans say.

I have added a few more pictures to the link above. I will take some of the motor mounting as well. Enjoy.