Steven Universe: Attack the Light Graphics Organization?

[Garamonde]

Hello guys. I have obtained the graphics for this game (thanks to Dinner Sonic) and after taking a look at them, I'm noticing an issue with organizing them into sheets. It is an RPG in which all the characters always appear on-screen at the same time (there is no party switching, so literally all the time, even during battles) and as a result, their graphics are all clustered together into different images. Not to mention the graphics are snugly laid out together so there's no real way to separate them unless a magic tool of some sort is used (some are upside-down, but that's just how they came in the data).

Examples:

So as you can see, the first one has most of the assets from the title screen (minus the background). That's fine, but then you come to the second one which has Garnet and Amethyst's assets clustered together on one image. Same goes for the third which has Pearl and Steven's graphics bunched up. Several are fairly organized/stick to one subject like the first, but they're mostly the ones that have the overworld tile assets and the backgrounds etc.; the rest however, like the characters/enemies, are jumbled with other things. There also seem to be several duplicates of things, main difference seems to be resolution and arrangement. I take it I'd just use the largest versions?

Examples of this:

Lunar Sea Spire enemies:

  

Can anyone tell me what I can do about this? I can't imagine the graphics would be usable like this.