Model rigging problem

For this model, every time I try to apply an armature rig the model deforms awfully like this:

But I want to make the model look like this:

I want this model to not have helper bones so I used the vertex weight mixer and transported the vertex groups of the helper bones to their corresponding primary bones. For instance, valvebiped.bip01_L_upperam and valvebiped.bip01_LUparmtwist. I then applied and removed the armature modifier, deleted the helper bones, and reapplied the armature modifier only to get the result of the first image. What can I do to fix this model? If you know of a way, please tell me what it is.