Thanks for the update. As I suggested in my comment, separate motion blurs on different layers might work for you.

Duplicate the layers to be motion blurred, and apply motion blur separately to each, then blend the two using a layer blending mode - in the example I used "lighten only" but you could experiment with others.

Example:

[![enter image description here][1]][1]

**Update:** Another alternative might be to use a layer mask to hide portions of the blur on different layers. I used a fuzzy brush to paint on the layer mask directly.

Example:

[![enter image description here][2]][2]


  [1]: https://i.sstatic.net/1WVsS.gif
  [2]: https://i.sstatic.net/NUI0A.png