Without seeing your skeleton it's tricky to say what the best course of action would be. However, this sounds like one of those early projects where it's probably better to start over than try to fix something that sounds like it might end up giving you some serious problems in the long run.
Changing your root bone scale in setup mode to something other than 1,1 can give you some problems as you've already noticed. Before doing anything else, I would set the root bone to 1,1 and export your JSON with non-essentials checked. Then go to Import Data
and import with a scale of 3.13. Your meshes will be scaled up to match, but you might need to set the scale of your other attachments to 3.13 unless your images are already the correct size.
You should be able to remove inherit scale
from your bones if they now all have a scale of 1,1.
Note you should save your new project after importing and set the correct Images
path for your images to show.
You might be wondering why you're getting the current behavior when unchecking Inherit Scale
.
Currently, your bones are getting the scale from the root bone. Their Local
scale is 1,1 but if you select World
you will see the scale is 3.13. When you uncheck Inherit Scale
their World
scale will be set to 1,1 which causes your bound meshes to get warped.