Then why is everything still messed up...it looks more messed up then it did before...(from a fresh download default setting)
Because the newest tile set replaces a number of the letters with more symbols. This was done in anticipation of all font being replaced with TTF support. Unfortunately it wasn't fully implemented from the start, so we have symbols intruding on our text in some places.
If you want to get rid of that you can revert back to an older version of the tileset save off the picture in the spoiler (first one I could find without uploading one, and should be relatively recent). You'll need to name it ironhand.png and replace the existing file in your art folder.
If you want to try and see how the animation of the water render, here is the 0.48 tileset with the 2 water tiles setup :
Of course, then some in game items will be replaced with letters, such as some parts of certain workshops and whatnot. But at least your text won't be covered in wells and various other stuff. I haven't tried this myself so if they shuffled around tiles things may be confusing in other ways as well, but I think it will be okay for the most part. Or you can just take the text tiles off of the above set and merge them into the new tileset.