I have found that using motion mixer is totally fine with w3d. What you need to do is save the scene with your original animation in it. Bake the ik part the fk can remain as is. Create the motion and save it to a file. Take the motion file and load it into a a scene with just the character and bones, it will animate normally and will export fine.
Here is a link to a character I did in shockwave and motion mixer
just extracty the files and run the exe. You can also put your own characters in here to test the animations. Just make sure your base t model is in the top level and put your animations in the folder below. I will make buttons to apply the motions for you to view. THe camera is dependant on how it looked in the t pose one
I would also recomend to save file size etc that you should export the model and animation in the base file (like the t pose) then just export the animations only for the animations and tell director to just call the it from the w3d animtions.