All of the above things are not in .cfg files as far as I know.
I don't remember off the top of my head, but the contact lines and units are .tga files in the data/menu/gui folder which have been replaced with files which remove contact colours and make the bearing lines invisible. You would have to find which files they are and replace them with original SH3 .tgas.
The UMark.tga is in the data/misc folder. Simply replace it with the original SH3 file.
The water colours are in data/env/EnvColors_Atl.dat. You would need to use a data editor such as skwasjer's s3d. That could get a little bit complicated.
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