As for figuring it out.
HEAVY SPOILERS DO NOT READ UNLESS YOU FINISHED THE GAME
Dylan stole the money from Jim's Comics. It wasn't in the register, since you can't store that much money in a register. It was stashed somewhere back behind the counter, in a place Dylan discovered while shadowing Jim at work. Only Dylan knows how to access the restricted parts of the shop. They hid the money for later, thinking that Gram wouldn't find it. She did.
Miss Walsh stole the remaining money from Dylan (which she got Lena to hide for her so she could intentionally get herself arrested and ensure Dylan wouldn't ever be caught. She figures that she's a sick old woman who's lived a good life, and she doesn't want Dylan's future ruined if they end up getting caught.)
Lena stole no money, but she did steal a camera and a computer from the shadowy figure who was trying to blackmail her. She didn't tell Dylan or Miss Walsh about it, because they both worry too much (in Lena's opinion). This information didn't make it into the game, since I didn't want the jam version to be too dark, but the stalker is actually Jim's "business associate", and that's how he discovered Lena exists. He's often in the back of the comic shop, and he sees her coming and going. Lena has figured this all out, and she's hoping the computer and camera footage ends up getting him and Jim caught for their crimes.
Jim is involved in a lot of shady business. Counterfeiting, drug dealing, and pimping people out through the comic book store as a front. He can be processed as a "thief" in the game for his sale of a fake Green Lantern action figure to Lena. Why did Lena want a Green Lantern action figure? It was supposed to be a gift for Dylan (not in the text, but you can guess this by looking at Dylan's character art).