You're going to have issues with duplicate product and category IDs which are, of course, not allowed. So if you get your two inventory tables merged, you'll then have to rebuild the cats_idx table and the set the category counts correctly. The fixCatCount mod at CubeCart.org can help with the two latter issues though.
If you can't seem to get it straightened out, there are several of us who have the CC & DB experience to merge the two stores. If you have a look at cubecart.org, you should be able to find a programmer who can do this for you.