For your item that gets damaged when using it in a crafting recipe, you could use this in your item file:
public void onCreated(ItemStack par1ItemStack, World par2World, EntityPlayer par3EntityPlayer)
{
mod_****.ItemBeingDamaged.damageItem(how many uses, par3EntityPlayer);
}
Not 100% sure if it will work since I didn't test the code before giving it to you but it seems like it would work.
Edit: Nevermind, this won't work since the item will be used up in the recipe. Doh!
But, still using the onCreate method, you COULD instantiate a private variable that keeps track of the ItemBeingDamaged current damage, and when the new item is created, give the player a 'new' ItemBeingDamaged, then call damageItem(current damage + amount, par3EntityPlayer); on the 'new' ItemBeingDamaged ItemStack