Lily Grinding with Noire (or any character with a Support/Heal skill) is actually pretty easy though boring as all get out.
Stock up on SP items, you'll probably need a lot of them.
You want the 3rd Stage in Chapter 3 (the one where you collect Moon Grass), kill all the enemies, and arrange the 4 characters you want to grind in a cross around Noire and have her spam her 2nd Skill (Muscle Memory?), when you run out of SP just use an SP item, every use gets you 1 Lily Point with your four neighbours. If they have support skills they can use them too, to get you 2 Lily Points per turn.
Just make sure you've got the height and attack requirements to actually get the Moonflower, I'm pretty sure that its possible to toss the crates such that they aren't retrievable if you're careless and its trickier to do it right if you only have 1 Jump or are using Green Heart since her attack has no height tolerance.