Yeah, like Statyk said: combine everything into one mesh (mesh>combine). Don't forget to delete history and clean up your outliner after that, Maya makes quite a mess whenever you combine or separate meshes!
Then open up your UV editor and arrange everything so that it fits into the square. For example everything that should have the wall texture in one corner, the roof in another...you get the idea. You might need some additional polygons in the walls and roof to make it possible to tile/repeat that smaller piece of texture, though.
After that, you make a uv snapshot that you can use as reference in photoshop. Make a photoshop file that's, say, 2048² pixels and put all textures you need in there as layers. Scale, crop and rearrange them, until they are in the place where your respective UV pieces are. (Roof texture on your roof polygons, etc...)
...and that's pretty much it!
I have to say though, it seems a bit odd to make a whole building one big mesh... it's not unusual for big structures like buildings to use several tiling textures at once. Since hpl doesn't allow multiple textures on one mesh (or at least I don't think so) having it in separate "sub-parts" actually makes sense...
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[MDL ED] Merging custom entities textures into one?
