I've done a handful of them, including the top on my FJ40 and my trailer.
Basically I start by doing any needed fiberglass repair to the top. Better to do it while it is still attached to the sides so it has rigidity. Then remove the sides, back and door seals from the top. Next drill out each of the factory rivets as cleanly as possible (you don't have to drill all the way through, just remove the head and then using a small punch pop the rest of the rivet out). At that point clean up the mating surface of the top, I've found a light wire wheel does the trick, being careful not to comprimise the layers of the fiberglass. Then clean and the drip rail, remove any broken bolts that you often find when you remove the sides & back. If your planning on repainting these items, now is the time. Next using a hi quality sealant (I use a bodywork specific white silicone), apply a layer to the top and a layer to the drip rail, not overdoing it. Mate the two surfaces and begin the riveting process. I use a bunch of nails to line up 15-20 of the existing holes. At the same time I am drilling out the holes to to a slightly larger rivet size than the factory. One by one start inserting the new rivets. Do the corners, then a couple across the middle, working your way around the top until finished.
Makes for a nice clean top: