fitted Custom Mesh Avatar with Custom Bone Structures

[HokaLate]

So I am testing a fitted mesh custom avatar, and it was going well when I left the second life skeleton alone, but then I decided "what if I needed to adjust the bone structure slightly, what would that do?" and I could have sworn I heard that it might be possible since people talk about giant and small avatars which I assume are custom avatar bone structures? Basically the avatar looks like below,

and a posed version of it in blender:

(just to note, when I export it to a .dae I select the option so it works for second life, and I make sure to select both the mesh and the armature so it exports both)

I was testing both major deformations and slight deformations, (the left leg was an anthro/furry wolf leg structure type, the right arm is to test what it will do with the slight deformation of the bone, and the left arm is to test if I made a major bone alteration the arm and bones are scaled to be 1.5 times longer). When importing, it looks like this in the importer, which is how it's supposed to look. 

so the arm looks like it will work, and I select "keep joint positions", and both "include skin weight"s, and the idle animation seems to work perfectly fine in the preview, but then when I import it and apply it to my avatar it looks as such (I'll post it with and without my avatar under it, so you can see that it's shoved the bones back up the arm, and on the image where it's edited with red lines, I've tried to outline the areas where it's obvious the lower arm was shoved back up the arm)

(edit: the last one is a new screencap that shows how it's just slapping the bones back to normal positions, since on the avatar's left arm it's just forcing them back)

and at this point I'm a bit lost on what to do, since the preview works but then in-game it shoves the bones back up. (the only reason the hand is longer than my avatar's is because it was scaled, but it's still nowhere near the length it should be)
Any ideas or thoughts? 

Edited December 23, 2017 by HokaLate
New screenshot to better show problems with left avatar arm

[OptimoMaximo]

When you do a custom bone position avatar, the scale of the joints/bones should be set to 1, no other value would carry through. So in order to keep your work in Blender, you should make sure to 1) in object mode CTRL+A Apply rotation and scale 2) in pose mode CTRL+A Apply Rest Pose (shouldn't be necessary, but you never know). Only problem comes with the collision volume bones, which have a individual rotation and scale for the  fitted mesh feature. You might want to try and separate them temporarily from the main skeleton, do the procedure explained above and then join the collision volume bones back to the original skeleton