I have searched the internet back and forwards looking for a problem I had with a mesh that I have and I was getting now where fast. I wanted to use an animation clip that I created with one character and use it on another character. Seems simple enough right? But the problem was that even though both meshes are in the standard T pose, I made a slight error in the construction of the skeleton of one of the characters. Instead of making a new skeleton for him, I copied the skeleton of one mesh and moved the joints into position of the new mesh that I'm having problems with now. The mesh works fine but the joints rotation is not zero. So if I character map the two characters, the animation would not be the same. I looked for ways to set the rotation of the joints to zero while leaving the joints where they are, but the only solutions that I found was an out dated plug-in for Maya 7 and 8.5 that says I have to rewrite it for my version of maya, and a forum that said to detach the mesh from the skeleton and freeze the joints rotation back to zero and re bind the mesh.
First, I don't know how to write a plug-in yet, and my character has a lot of different meshes that make up the character and that would be a long process to do. So I accidentally ran into this nice little solution. Just to let you know, this technique does not really set the joints to zero but it is a good work around.
Ok, if you look at my character you can see it is not so much in the T pose as it is in the creation of man pose. When I select the left shoulder joint you can see that the X, Y and Z rotation is not zero. Don't worry about these channels being highlighted, I just have key frames set for those channels.

Select your root joint and go to edit then duplicate special.

In the duplicate special options box make sure that duplicate input graph is not selected and click the duplicate special button.This will make sure that what ever it was that was stopping you from setting the original skeleton to zero will not effect the duplicated joint.

With the duplicated skeleton still selected use the move tool to drag the skeleton out to the side.

Now select all of the joints on the duplicated skeleton that you want to have a zero rotation and hold down the right mouse button over the channel box and select freeze then rotate from the drop down list. Your joints should now be set to zero.

Make sure that your menu is set to animation and choose the constraint menu and go to parent constraint menu option.

Make sure that rotate all is the only option selected. Maintain offset really isn't important. and close the option.

Now select the duplicate left shoulder and shift select the original left shoulder and apply the parent constraint. If you rotate the duplicate joint, the original joint and the mesh will rotate with it. Repeat this process with the other joints but instead of continuing to go over to parent constraint just hit g to repeat the last operation. after you finish parenting all of the joints just move the duplicated skeleton back to where the original skeleton and hide the original skeleton Now you can use the duplicated skeleton with joints set to zero rotation instead of the original skeleton
