You cannot make cocoa beans. They spawn naturally in jungle biomes on jungle trees. You can also spawn them via creative mode. Hope this helps.
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You can craft cookies with cocoa beans by putting cocoa beans in between 2 wheat in a crafting table.
As of Beta 1.4, cocoa beans couldn't be found ingame. You can only find them inside dungeon chests. You can read more about dungeon chests on Minecraft Wiki (the link is under "Sources and related links" below this answer).
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There is no 'brown dye' - to dye wool brown, you just place it along with Cocoa Beans into your crafting slot, to make Brown Wool.
I didn't make Minecraft.