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Here's some tips.
>1.
You got to be willing to go the distance. 3 boxes is only 90 eggs. It's REALLY rare anyone gets a shiny in less than 100 eggs. You better settle in for the long haul.
>2.
Fill boxes wastes time and box space. You're better off just upgrading your Join Avenue until you get a Rank 10 nursery which brings me to
>3.
In my experience the best way to MM is this.
>Get a Rank 10 Nursery in Join Avenue.
This might take sometime but trust me it's worth it.
>Get a notepad and pencil.
Or just use a calculator or PC to keep track of eggs.
>Save in front of the Daycare man when he's NOT holding an egg.
Just go back and forth until you have 5 eggs.
>Then take those 5 eggs to the nursery and do the LV 5 warms.
If none of those 5 are shiny the just soft reset, and rinse and repeat until you get your shiny.
tl;dr Just save infront of the perverted old man at the daycare, get five eggs, got to Nursery in Join Avenue, warm there, and Repeat till shone.