hello Drakkhen20,
you can use whatever you want from M.E.P but have in mind that 'mixing' things is not so simple as it looks and ,also, i wouldn't recommend to do so ...unless you know what you are doing !
anyway...if something goes wrong will not blow anyone's pc so give your shots !
about your questions : for altering the water's color is a combination of many things (at scene.dat ,skycolors.dats and envcolors.dats) BUT the basic and more 'effective' settings for the water are the 'waterlightcolor' and 'waterdarkcolor' inside the envcolors.dat and the specular.tga image inside the skycolors.dat
these are the basics...so you can start from there
about the really annoying ''polygon effect'' is something that is unsolved till today. i am almost convinced that the solution for this is 'hiding' somewhere in executables files so i believe that only people who can 'look' inside these files can 'heal' this bug.
good luck
