Yep, you first need to find a convertable Samurai to get an idea of exactly what you are getting yourself into!
If it was me and I lived in California (at least the parts where it don't snow like crazy), I would fab (or have fabbed) a fabric top. If the metal part of the top that crosses overhead behind the driver's seat has been removed, I'd first fab a replacement for rollover protection AND to support the fabric top at that point. Unless you are planning for folks to sit in back, I'd get a bikini top fabbed at local boat cover shop using snaps around the edges to hold it in place. You might be able to use snaps across the front windshield with some sort of hard insert sewn into the leading edge in order to get a decent seal. Then you also have to seal the vertical edge behind the door in some fashion. Again, check a convertable Samurai to see ho it is done there.
To me your big problem is trying to make a functional top -- and adapting a Samurai soft top is not going to work very well.
Hope this helps!