A suggestion to help out with the mining aspect. It would be useful to have a gem bag, that stashes whatever single smelt gem you have. Those include Moonstone shards, sapphires, florescent gems, etc. Your main mining wolf can carry both gem bag and ore cart, but you can also add a second wolf to just carry the gem bag back and forth.
This would somewhat help with the mine cart clutter, and you could always either craft additional gem bags, or, expand the one that you have. (With Pebbles of course) It might not help out 100% with having too many of one kind of ore, but at least it would help manage the single drops a little easier.