Is there an aftermarket covered gear box that comes on the newer X's that I can get for my '04?

Don't think so. I wish I had my 01's box... it was larger and could actually hold stuff in it. My box has now become a perfect spot to put all the dog's stuff in it for trips... food, bowls, leashes, etc.

Check the size of the 2nd Gens vs. 1st... they are very different.