A friend did this with a Trojan, I think.
He cut after the "turn up" and used that as the base for the gunnels. He laminated wood under neath to make them wider, then flexed a plywood skirt around the interior as the turn down that would support the coaming pads.
Once that was all solid and strong, he trimmed the turn up section, routed the inside edge, and glassed it all in. It went faster and looked better than I ever imagined.
Then he made a front platform using the original bunk area, with storage below, which was relatively easy, and all turned out well.
I never saw in person, but it looked like a success to me.
My advice is to think very carefully before you cut. You may be able to build much of the structure before cutting anything, from inside the cabin. That would be ideal, to prevent excessive spreading and settling.
It's a lot of work, but I hope it works great for you!
