The grouping tool can do a lot, once you're used to how it works, but it has a few quirks. If the door is visible on the texturemap, you can do a lot with a paint program -- I use a quite old copy of Paint Shop Pro. What you're trying to do is take the texture map and convert it to black-and-white. The white parts will be visible, the black parts transparent, when the result is used as a transparency map. A dark grey is good for windows -- not 100% transparent. How to do that conversion? I'd recommend you look at how "layers" work. Put the original texture as the background layer, and paint the transparency map on another layer. If the doorway doesn't match the model's mesh, there's no advantage in using a UV template as a guide.