I've gotten a lot of the ideal gameplay worked out with a spiral notebook containing all of my notes. My current blockade is working out dynamic hitboxes for things like weapon swings and spells in real time, instead of in a turn based format. I've tinkered with it in a couple different test projects, but haven't found a good way to create a sort of general form of it that I could use in multiple games as a simple add-on.

Hm.  This might be something worth adding as a standard library module.  Hitboxes are a pretty generic thing so it's a good candidate for a pack-in module that all games can use.

For implementing it yourself, I feel like maybe you could ask Radnen for advice here.  His Blockman game uses a real-time battle system similar to Secret of Mana so I know he's had to deal with the problem of hitboxes and such.

  gotten a lot of the ideal gameplay worked out with a spiral notebook containing all of my notes

Next part would be to outline a working battlesystem -- the dynamic Hitbox feature is a problem for Sphere
There is a program called Mugen that allows this but it is more focused on sidescrollers than top-down RPGs

If intended on using Sphere, it's possible to cut or simplify certain features to remain
Otherwise it's possible to use/switch/replace spritesets in-game for variation between hitboxes -- checking for overlap from enemy sprites on another layer

been considering moving away from sphere to make use of 3d models

If you're able to sketch/draw, then deal with the workload it'll certainly be recommended but I would seriously consider sticking to 2D for simplicity sake

I am bad at spriting animations still

This is certainly some area I can help in for free -- send me some screenshots/concepts with tile/sprite/resolution size and I'll certainly pitch in.

The main idea here would be to think of the project as a sum of parts rather than finishing as a whole