The biggest challenge for the homebuilder will be how to finish the inside of the top, and how to attach things to the top. On our van, the builder glued wood stringers on the underside of the top and then attached the ceiling plywood to that with screws. They used silicone caulking for glue. I'm not thrilled with the idea but they would fix it if it falls down.
On a previous build, we used a Fiberine top with a Fiberine fiberglass headliner. That gave really good headroom and a spacey feeling, but was a little cold and very noisey. It was also difficult to attach things to the top.
I think the best homebuild option would be to have Fiberine or another fiberglass shop build the top and have them glass in 3/4" plywood pads wherever you need ceiling supports. Then install the top yourself for a good savings in labor.
A lot of used high tops have steel roll cages, which reduce head room substantially.
Our 24" top cost $2500 installed, plus $450 for a window and $1,000 for paint.