I am a moderator at
www.coloradoK5.com 
Making the 76 up K5's into full top / roadsters is pretty comon. I own a Roadster K5 and love the topless thing but hate the MPG.
Here is what most people do when making the conversion. Full roll cage tied into the windsheild frame. That simple. Now to make it even simpler. There is a kit available to make a Toy truck into a convertable and the hard top can be reinstalled. I have helped make Such a conversion. It comes with a fill peice to join the roof to the windsheild header. At the B piller you would need to make a plate and some sort of latch. Really wouldn't be hard with the kit and a welder.
As for the window frames:
The kit address this in one of two methods. I would recomend using the vent wing doors to add some stability the cut of above the vent wing. bulb style gasket is then put on the top to form a seal. The seocnd way is the window track that is cut off is welded to the roof section then cut away and a thin gasket used. This actually has better results because the gap is smaller but you get the idea.
There is also a Targa kit available. Check in Truckin Magazine. Places like Godfathers sells these kits.
When I decided to go from K5 to the 4Runner I had to have the Sunroof for basicly this reason. I loved my full convertable and running topless. Seemed pointless to take the half top off on my 79 Blazer because that still left me under a roof so I never did. Now I can just pop the roof out and while not as open it still is close.
