Thanks!
Thanks too for the advice regarding map_c tools guys. After a bit of fiddling around I was able to modify the coastlines successfully. Later I'll be able to detail it properly using satellite images for reference.
Still having problems though with some areas (see below). For example, Simpson harbour keeps the green beach no matter what I do to the map_c. The coral texture stops dead and can't be added. It must be caused by a different file methinks. Other parts of the coast have similar problems. Any insights will be most welcome.
If I am understanding your problem correctly, and if you are working with the layered file in photoshop
Open your Map T, choose "Magic Wand Tool", select water area in map T, then choose "Select>Modify>Expand" make it expand by 1 pixel (now the selection will overlap your land by 1 pixel). Make new layer, apply RGB value for "Water3" (thats usually the beach) on that layer/that selection (or you can apply any other value that you choose for your beach texture). You should have beaches then, and if need you can correct them later by hand.
In the same way chose water areas on map T, without expanding and add RGB value for water, on top of the layer for beaches.
For corals, you must paint areas where you want them on your map C, but you must also paint RGB value for its texture to the same areas on your map T (usually the RGB value for "Water2"), otherwise the game wont show them. The painted area must not be too big in one take (in a block), or game wont show it again, so chop it in several smaller areas or erase some areas a bit (no need for 100% of opacity for eraser tool, play with it).
For the woods, you can use some repainted (I have one too) and you can make their colors according to you needs, or you can even mix the layers from different sets (gives more random natural look).
Something like this:
[WOOD]
Wood0 = forest/summer/Jungle0.tga
Wood1 = forest/summer/sk_Wood1.tga
Wood2 = forest/summer/sk_Wood2.tga
Wood3 = Italy_DF/forest/summer/itawood4.tga
Wood4 = Italy_DF/forest/summer/itawood4.tga
WoodMask2 = forest/summer/ForestMask.tga
WoodMask3 = forest/summer/ForestMask2.tga
WoodMiniMasks = forest/summer/MiniMask.tga
SideWood = forest/summer/ForestSide.tga
Oh yes, you can also lower the value for red in the water line: (the red numbers)
[WATER]
Water = water/PacificWater.tga
WaterColorATI = 0.070 0.155 0.275
//WaterColorATI = 0.100 0.175 0.230
WaterColorNV = 0.000 0.155 0.275
//WaterColorNV = 0.100 0.185 0.268
You'll have more natural water, not so "Baltic dark purple"
Hope that helps a little bit