So i was having problems with the shoes until i found away around looking in the files of my game.

1. use the model manipulator on the shoes.

2. paint one of the default shoes (only one of the shoes) in the "enhanced inkling" set with the hat painter tool.

3. paste the manipulated model on to the one shoe.

4. bonemerge the effect to your inkling. (There might be some minor clipping with the feet)

(If this sound confusing please ask me to clarify)