Eric,

What you are doing is a big no no... All the scaling and stuff needs to be done before skinning and weighting. Once thats done you should not deform, use blend weights or manipulate the geometry in any way.

Best to detach the skin and get all your scales right first then re skin, re do the paint weights, you should not have to re do the rig that should br fine.

Sorry to be the bearer of bad news, but needs must.