The key here is to “PLOT ALL” of your animation in Motion Builder.
First create your full body ik
Next import into MB
Next drag you mocap data into “story” tab inside the “Navigator”
Next AND THIS IS KEY go to the “Animation” tab at the top beside edit and “Plot all”
Next delete you mocap data from the “story” menu in your “character track”
Next play to make sure you animation was ploted on you skeleten
Next go to “File” and click “EXPORT”
Next name and export via save as type Kaydara (animation only) (.fbx)
Next go back in Maya and “import” the saved (.fbx) file

My Settings:
I’m using Maya 8.5, “FBIK JackieSkeleton rig” (Maya’s FBIK example), FBX Import plug-in 2006.11.2 for Maya 8.5.
My importing settings are an Exclusive merge, Resample as Euler, Use FBX frame rate, Merge animation layers, Import Geometry Cache, and Show the Warnings.