If the shoe has a corresponding body part with the figure (left shin figure=left shin shoe) scaling that body part by the same amount as on the figure will do the trick.

So if you increase the yscale on the figure's shins to 110%, then selecting the shins for the shoes and increasing yscale to 110% will line them up the same as if they were both at 100%.

The other option would be to save the figure with the rescaled legs, import the .obj for the shoes, position it where they should be, and take the shoes into the Setup Room, loading the bones for the rescaled figure, and go back to the Pose Room. That should work fine, although it's more complex depending on how you scaled the character's legs.

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