One of the first things you want to do in motion builder is make sure you don’t have any breaks in the markers or any added markers that are not part of the character this is called the first pass of the clean up process.

 A lot of animators will place the actor inside the markers, add the markers to the marker set, and then leave it at that, you can also tweak how the actor sits between the markers, after the marker set has been activated.  The great thing with motion builder you can make animation layers easily and make tweaks after your character rig has been imported and driven by the actor.

This is great to help solve issues like your head/neck problems, or problems with arm twist that are difficult to judge clearly from the T-pose. Fixing these small problems is faster doing in motion builder than if you were to bake out the animation and try fix it up in Maya.