I think you'll probably have to use targa, but I am not entirely sure how PNG generates its mask. It'll be easier to work with on TGA though because your transparency mask will be separated into the alpha channel. There's a lot of ways to fix it, you could just paint into the empty space of your texture. I would just use…
Looks really good so far, you need some edge padding though, especially on your leaves since they're masked. Also I'd suggest uploading your images to imgur or dropbox then linking them, you'll get more replies than using attachments since people can't view attachments unless they're logged in