If you didn't know, After Effects has these things called "Layer Styles". These are similar, but are NOT the same as effects. As layer styles are applied after everything else. 
I will go more in-depth about layer styles in a future tutorial, but this should give you the basics of all you really need to know right now.
Clicking on stroke you can see that it will apply a very simple "outline" effect. If you've ever used a program like Photoshop this might seem familiar.
However you seem to notice something when motion blur is applied. 
The motion blur does not effect the stroke style we added. :(
Luckily for us effects are here to not make us bang our head against the fucking table.
Copy my settings here. 
All this basically does is "mask" the transparent part of our clip with blue, Keylight will key out the blue, and the "Screen Matte" will expand the key-ed out background and replace it with the "Replace Colour". You can mess with the settings if you want. I would also recommend creating a user-made-preset since you might be using this a lot.
Seeing as the effect is now applied BEFORE the motion blur, it will now be effected by it. 