I have a 1950 Ford Buisness coupe which I plan to chop the top and have seen two doors that were made into hardtops in magazine pictures but really don't know how to work out the back window and the weather seals
I live in the UK so the terminology may be different, but if you want a pillarless look, the idea about making the quarter windows slide in is a good one. But, if you want a good weather seal too, cut a strip of glass and attach it to the inside leading edge of the quarter glass using a silicone type adhesive for fish tanks. The good thing about this adhesive is that it will not discolour. Then, attach a thin strip of rubber to the face of the strip of glass so that when the door is closed, the door glass sits against it giving a good seal. Hope this helps.
McMASTER-CARR sells a bulb type seal which has a channel you could slide over the edge of the glass. This is available by the foot and the location of the bulb and channel width is offered in various combinations http://www.mcmaster.com