To exclude any object from the toon ink lens shader, in the ppg set it to "require host" under the ink tab (I'm not in front of it so it could be under another tab... just look around). That way, only the objects with a toon host node in the render tree will have ink lines. You can plug the toon host anywhere on the material node, so just find an empty slot if you still want to preserve your original shading and still have the lines...
For the smoke, check your alpha channel: it's probably very dark. you can check it in the render region. You must have set it to render with a non-premultiplied alpha. If the pass contains no colour and is just greyscale, you could always comp it using its own luminance values. Or you could try multiplying it over the top, or doing an add... just play around with the maths settings... 