How do I make a new rest pose when using wieghts and MeshDeform? I want to change a relaxed posed rigged character to a T pose. But a new complication arises when the character has both weight and a deform cage. 

For modifying the rest pose without MeshDeform I do this:
1) In “Object Mode” select your deformed mesh.
2) In the Object Modifiers stack, copy the “Armature Modifier” by pressing the “Copy” button.
3) Press "Apply" in the top one, but keep the bottom one.
4) Repeat steps 1 and 2 for all mesh.
5)  Select your armature and go in “Pose Mode”.
6) In the “Pose” menu “Apply Pose as Rest Pose” 
7) Select your armature and go in “Object Mode”.
8) Apply rotation and scale &amp; Apply location.
9) Same for all the mesh.

If you do that with both system as soon as you copy one the mesh flies off or the cage flies off.

I don't know what to do and what order to do it when you have a mesh deform cage and it is also rigged with weights for the fingers and hands. 

So what steps must I take to create a new rest pose?
There are almost certainly multiple ways to set up a mesh deformer and an armature, and there are things that seem like they should act like mesh deformers but don't really.  Different techniques demand different solutions, so you have to understand your particular model first.

Let's take the example of a model where it is being deformed by a mesh that is being deformed by an armature.  I'll skip local loc/rot/scale-- really, your armature ought to have a root bone so that you don't need to have any local loc/rot/scale on the object level.



1) Select your object that has a mesh deformer modifier.  Copy the modifier and unbind the copy.  Apply the original mesh deform modifier.

2) Select your deformer-- the target of the mesh deform.  Copy the armature modifier.  Apply the first (top) armature modifier.

3) Select your armature.  Apply pose as resting pose.

4) Select the object to be mesh deformed.  Hit the bind button on the (copied) mesh deform modifier.