Ah, I should be able to help out, though I might point you to UR's nice new Art Requests thread. I admit that it's getting a bit late where I am and I'm a bit tired, but in the morning I should be able to do some drawing. One or two things though:
For the first image, I'm assuming you mean shadows cast by the pipes onto the brown 'cave' tiles. If the shadow is cast to the right and down, then extra tiles would have to be added exclusively for shadows. I might suggest changing the tiles so that you only have one horizontal pipe, but that's from a tileset maker's perspective, not a tileset converter's. If you aren't too worried about tile-for-tile accuracy, then that would be a good way to go, I think.
For the second and third images, I'm not quite sure. I can see what you mean by not quite looking natural, but I don't really have any ideas on how to fix them.