Made a little bit of progress…

The story's really coming along nicely. I have the majority of it planned out, but obviously details will have to be figured out when I get to them.

I've come up with a plan for how items and shops will work that I like as well. Basically…
Traditional healing items like potions and ethers will be super expensive at the start of the game, but food items like apples will be really cheap. Most of the player's money will come from either chests or selling useless junk that drops from non-human enemies. E.g: the various colors of goo you get from slimes can be sold at various prices, depending on the color, since certain colors are rarer than others. Human enemies will drop money, but they're only found in very specific areas and scripted battles.

This is a bigger project than I expected, but shouldn't impossible…although there will be several different endings and I'm considering a special alternate story path that will change the story a lot for players who choose it.
The way the "endings" will be set up is a little like Fallout 4 (except less lame) in that, at some point, you'll have to choose which faction to side with. That faction will help you and the ending will change slightly. However, the characters you have in your party and which faction quests you've completed will also effect the ending. E.g: If you finish the Crimson Knights quest-line and have Bruno and/or Lana in your party when you fight the final boss, the ending will change slightly. This means that, if all quests are completed and all allies are in the player's party, they'll get the "perfect" ending, which is a combination of all other "good" endings.
Like…a modular ending. Having certain allies will add certain parts to the cutscene, rather than change it altogether. This will be true for the rest of the game as well, but here it will have a much bigger impact.