I thought hard about doing this myself with my old two door. A couple of things to keep in mind:
The roof is structural in those trucks. I had a parts truck with the roof cut off, and the doors wouldn't open and close because the body was so flexy, and it was rust free. You'd definately have to build a cage in it.
The roof is only very thin tin. A few times on and off, and it will probably warp beyond putting back on.
I don't know if they are still in business, but there was a company in the past that had a cali-style kit to remove the center section of an S-truck (think t-tops without the center bar) I thought about using one of those kits, then whacking the rear of the roof off, and having a canvas top built at a boat place for the rear. When all the top material is off, it would only have a targa bar like a samurai. I think that would look pretty cool.