Using the jk8 body parts gets you almost there. The challenge is making the custom top in a way that it will meet or exceede the longevity, quality, and features of the stock quality top.
I haven't studied the factory JK hardtop enough to know how much work this might be, but it seems to me the factory hardtop could be modified to have removable side panels, and a set of new side panels could be made to run all the way up to the back of the front door (or probably to the front door jamb from the back door). I think you could cut off the sides of the factory hardtop, make molds for new upper sills to finish off the cut-off bottom of the roof panel, and then make molds for longer, removable side panels.
Door filler panels for the lower part of the rear doors would be pretty straightforward to make in fiberglass, although if you really wanted to do this right, you'd use the seamless JK8 panels instead of filler panels where the door outline would show.
Based on my experience of building a modular hardtop completely from scratch, I think it would be reasonable to build a "conversion kit" in fiberglass that would offer the following options:
- Modular, removable side panels; both hard side panels and roll-up soft sides could be options.
- Factory length side panels for those who want to keep four doors.
- Longer side panels for those who want to do the 2-door conversion.
- Lower half rear door filler panels.
Just for reference, the rough parts for the LJ modular hardtop:
And those parts fully finished and installed: