Hi Murasaki! Haven't seen you for awhile! ^_^
Nope, I don't think I've ever posted anything on gamefaqs, though I do go there once in awhile to look stuff up. I post here a lot (though only recently got an account on fogu - previously was a fishy for years), and I use the same username on fanfiction.net and deviantart and a long, long time ago on TSR, but that's about it that I can ever recall.
Anyway - you're right, there is no "sorting" function in your storage. Everything just goes where it goes. That's why you have to kind of juggle items in order to manipulate which stone becomes the base for your ore stones' star-level. Here, I'll explain more:
I think of what's in inventory as a "stack". The "bottom" ore stone on the stack is the first one, that controls the star level of the entire stack. Any new ore stones added on top of that stack take on the star level of the stack.
This works with ore stones because until you smash them, the star level is hidden, so the game stuffs all your ore stones into one stack regardless of their original star level and behind-the-scenes forces all their star levels to be the same. Unfortunately, as far as I know, nothing else has "hidden" star levels like this, so you can't pull this trick with anything else - everything else will still go into separate stacks if it is different star levels and you can't combine them.
So...if you want to change the first ore stone in the stack, you need to get a new stone that you know is good - e.g. the bonus reward ore stone from Sheng's watering/harvesting requests that is guaranteed to be 4-stars. Then place that stone on the ground by itself so its star-level won't be "contaminated" by any stack. Then take out your old existing stack (or stacks, plural, if you have some ore stones in both your rucksack and your cart/storage) and set those on the ground. So now you have 2-3 ore stone icons on the ground - your single good stone, plus the stack(s) of whatever you had in inventory, and you have no ore stones at all still in your inventory.
Now, you pick up your single good stone, and put it in your rucksack or cart/storage. Because you took out your other ore stones first, your new stone is the only ore stone in there, so it will be the "bottom" of whatever stack of ore stones you put in after that, and will force all those stones to match its star-level.
So now you just go pick your old stack(s) of ore stones back up again and plop them in to your rucksack or cart/storage on top of the new stone - make sure you put them in the same place your new ore stone went - and voila! Now all your ore stones have the new star-level.
Did that help clear anything up?