Are you planing on keeping the hard section as the top, or using cloth/ top material?
One of my friends cut the top off of his Ranger (it was rolled when he got it, so off it went) and the the thing has horrible body/ frame flex offroad now...
But then agian, your's has a 2.3 not a 2.9 like his, and I doubt you take it off road.
I think it would just be a matter of folding/ fabricating a lip out of fairly thick sheet metal (slightly thicker than what your doors/ hood is). I'd take the sheet metal and make a lip for both the top of the windsheild, and the cut out section, so that it slides/ fits together nicely. And you'll have to get some cam-style latches or soemthing to hold it to the main part of the body when it is on. And other than that, I'd just get somethin like weather striping for the trunk lid of some car, and use that. That way you have plenty of lenght without having a seem in the middle of the roof.
Would you be getting rid of the upper edge of where the door frame goes up next to the cab-roof, or would it be like a giant removable sun roof and only be a hole in the roof?? Some more info would defentally help alot.