"it has discolored coolant (dark brown in the overflow bottle)"
Change the coolant.
http://www.contour.org/mods/mods.php?s=howto&displayid=44
" and the trans fluid appears thin."
Change the ATFluid. It is hard to tell if it is thin as the ATFluid looks thinner than your regular engine oil.
http://www.contour.org/ubbthreads/showflat.php?Cat=&Board=tranny&Number=992476&page=0&view=collapsed&sb=5&o=31&fpart=1
" I am also going to replace the water pump (2.5L motor) but I forget what is the preferred color for the improved impeller design."
Metal or white plastic impeller.
http://www.contour.org/ubbthreads/showflat.php?Cat=&Board=v6maint&Number=1132376&page=0&view=collapsed&sb=5&o=7&fpart=1
