If you are going to over plank the deck, they why not check to see where in the rear superstructure it can be prised up or even dremeled off, any repair to the superstructure sides will be as easy to do than trying to convert it to the space ship, as would RC conversion, with careful planning, all the rear could be removed and replaced after stripping off the decking as you were planning on repairing this by laying another layer on top.
If you have the books then, knowing where the structural bits are, will help you to find the best places to cut.