I have an edited skeleton that works near flawless for a mod I am working on. I am having 1 major problem I have made it so my character (race) is kinda short and squat yes its a dwarf. NOT A DWEMER.
My problem is the legs just will not scale. They stay normal size and look kinda funny. How would one go about making the legs "fatter".

if your race has its own skeleton that isnt shared with any other race, you are better off creating a cusom body mesh for it and don't use the default character body.

you can model this to however fat or thin you want so long as it's properly weighted to the skeleton

Depends on the 3D application you are using. If it's 3ds max you would need to go to the bone tools and scale them there. I don't know if that will break the animations though. I think it would off set the timing of animation if it didn't break it. I haven't yet done anything with animations and skeletons in Skyrim due to lack of Beth support (behavior files) but this is how I would approach it. This is all of course if you're are trying to scale the bones.

I use a modified skeleton by scaling the existing nif in 3ds max but I cant seem to export it, the file always comes out as file size 1 byte with only the header info. The body mesh I can edit end export no problem, trick is getting the neck hands and feet to match the mesh properly. Oh well I may take a break for a couple days then go back to it. Thanks for the help.

There is a thread around here about custom animations you should look at for exporting. It should tell you how to export the skeleton out. Sorry I can't be of any real help