Yikes!
You got some work ahead to fix this guy.
Just kidding! It isn't that bad. First off I would recomend that you avoid scaling group layers or bone layers within an individual character. I know it's tough but you will thank yourself later trust me.
When you scale group layers the way you have (head group is scaled up, the parent folder is scaled down) you will have a hard time maintaining consistent stroke widths and relationships to all the parts. I know this guy doesn't have strokes but you may do that at some point and then it's a nightmare to match them up or get what you expect. If one group is scaled one way, and the stroke width is say... 2, then another layer in a group also has a stroke width of 2 but the group is scaled differently the strokes won't match. Also effects will render differently.
Seems silly to worry about that but that is my personal opinion. I did that sooo many times early on and kicked myself later for being so stupid. Having all these bone layers for one character with a different scale just caused headaches. It was best to draw the character all at once just the way I like it and THEN split it up if I need to.
It is much easier to keep all the parts of one character the same layer scale. Just scale the points instead.
Having multiple layers is okay as long as it doesn't frustrate you while working. This is a very simple character so putting all the elements on just a few layers would be fine. A different layer for the head arms and body would be a good place to start with this guy.
The next step is to pull all those layers out and rescale them to match the group layer scaling.
This is very very easy. Just duplicate the whole bone layer of the whole character, pull all the parts out of the group folders and then use the original that you still have underneath the new one as a "template" to scale down the vectors to match it.
You could copy and paste all the body part vectors into one layer to make this even easier before you start. You can easily separate them out again if you like working that way. Just duplicate the layer and delete parts. I do this all the time. If I have bunches of layers and want to scale all at once I just copy and paste into one layer, scale the points, copy them out again into separate layer. It doesn't take that long.
Once you get to that point, with the head as a single vector layer, the arms a vector layer, the body etc etc... they should all be children of one bone layer. THEN you can do bone binding if you like OR you can do flexible binding if you like. This gives you more choices.
You could even have bone layers with body parts under the main bone layer skeleton if you want. I find this is great for hands. Sometimes having all the fingers in the main skeleton is a pain. Put the hands in a sub bone layer bound to one hand bone in the main skeleton. Usually you do broad animation of the main body then you can go in an focus on the hands. That's just my opinion anyway.
I don't think you need my bone slave script for a simple character like this. It's up to you later if you think you need it.
Wonderful character by the way! Reminds me of the guy in the yellow hat in "Curious George".
-vern