Well if you are going the rout of just closing the window with sheet metal then lucky for you, when you take off the side panel, there is no calking to be had. Due to toyota's good planning there are just a series of 10mm bolts that go around the edge of the window. Once removed you press on the inside of the window and it will pop our, leaving you a gooey tar like substance that was used to seal the window, you will not need to replace this due to the fact that it isnt a hardened seal, so all you have to do is cut the size of sheet metal you need, then send bolts through the edge and into the already placed reinforcement bolts through the frame of teh window (: no calking or anything tricky like that.
