For those still having trouble, a quick guide:
Scene #1 (Marionette first time) visit Marionette. Simple enough.
Scene #2 ( Marionette Threesome) Look in Marionette's trash for a broken part, combine with one of the parts in the bag you bought from Mona. Give working part to Marionette and wait a day, then come back.
Scene #3 (Mona First Sale) Keep Grinding the Marionette minigame until you can buy the first item from Mona.
Scene #4 (Mona Second Sale) Keep Grinding the Marionette minigame until you can buy the second item from Mona.
Scene #5 (Xavielle's Ritual) After buying the second item from Mona, give Xavielle the pebbles and the vial of bat hair.
Scene #6 (Breeding Worms) In the northern section across the bridge, go to the house to the west. Find a note in one of the pots, then interact with the fish statue. When that fails, go around outside to the back of the house and turn the valve. The valve will break. Keep Grinding the Marionette minigame until you can buy the third item from Mona, a wrench. Fix the valve, then press the button on the statue again. Wait a day and come back, then use the chain on the pool. Then go for a swim. After the scene, wait a few days (a week?) and come back after Yu says it's time to go back (you'll see some new dialogue when you go back home). Swim again, and the option will pop back home.
Drawing #1 In a trash can outside one of the southern houses.
Drawing #2 Interact with the green glowing plant in the south-east corner.