Alright.
You've definitely made progress, but you've also made a few mistakes in formatting. We'll start with the weapon.
The Woodsman
Level 5
Attacks Per Turn: 2
Affinities: Fear
Ability: Mode Change | Murder (handsaw) | Catastrophic Damage (chainsaw)
This is a copy of Red Hood's weapon data. As you can see, it is only placed once, with the mode specific abilities on the same line. This may seem a little unwieldy, but it helps save space when compared to what you currently have. All you need to do is place the Lights Battery's mode specific abilities with the name of whatever mode they go on in a single line, and you'll be able to upgrade all three modes at once. Given how you've set it up though, she likely won't get any new Abilities or ability upgrades for her weapons other than pure numbers for a while.
Now, regarding the spell.
Similarly to her weapon, you don't need to spell out each individual variation. Here's how I worked the Protean ability for an MG I created.
Cursed Bolts
-Fairy Huntress may substitute Protean on her Enchanted Crossbow with an Ability from the following list. She may freely change what Ability she is using, but cannot change the effect on any previously fired bolts.
Curse
Slumber
Poison
Chill
Stun
Double Tap
The bolded part is the important part here. Fairy Huntress has Protean on her weapon, allowing her to switch it out with one ability from a list. By placing the Abilities all under a single Ability in her file, I can upgrade her weapon while maintaining her ability to use the Protean Abilities. If you simply gather up the Abilities you wish to give Shining Spark access to at the start and place them in a list like I have for Fairy Huntress, you can upgrade the main spell and make it more powerful, while simultaneously making sure the Abilities can still be used. Just make sure that you specify in the ability that Shining Spark can replace Protean on her spell with an ability from the list, for the sake of being clear.