Download this file
http://users.tpg.com.au/jfwfreo/dummyart.zip
and unzip into the mod SDK art folder.
Basically it contains empty XML for all the art that comes from the main game files (i.e. all the art where the SDK will say "I cant find file xyz" but will still be able to pull the relavent art data in). This means that when you have it installed, the compiler will stop complaining about art that it cant find but which it doesn't need. Mods will still work because the files are empty so the compiler still pulls the data for the art in question from the game.