Coupe A pillars are not as tall as the wagon roof, and are laid back more.
The way to do it, IMO, is use coupe doors, and construct window frames from the front and rear door frames to fill the hole. trying to use the coupe roofrail weatherstrips would take even more fabrication, and the glass is not going to come close to being tall enough. Using the coupe windshield and pillars makes the roof low in the front, unless you bring it down all the way from the back.
There are a LOT of differences between coupes and sedan/wagons that most people do not see, aside from the number of doors. they're really two different animals, since the coupe is a hardtop style car (albeit with a B pillar and fixed qtr glass), and the sedan/wagon is , well, a sedan style body.
It can be done, obviously, but it's not the cakewalk many think it will be...at least not if you want it to look like a production car.
Best advice is to get a coupe and wagon side by side and bust out a tape measure...it'll become apparent very quickly the scope of the differences.