Hey. Substantial update there!
First off, about the problem with Lily's shop quest you could simply put her shopping as an event, and instead of saying to "bill it to the Sentinels", you could have her "hand over X ammount of money" to each of the shopkeepers.That would solve the problem with spending all starting money in trivial things.
As for normal shopping, you could then do the "normal shop processing event" whenever it isn't inside a quest, and as such, what the player buys is of no consequence.
If you need any help with the overworld, I'd be happy to lend you a hand.