You can try with a fade expression for the layers. After you apply it to one layer you can copy the expression and select random layers and choose "Edit" - Copy Expression Only.

Here's the expression:

fadeInTime = .5; // time (seconds)

fadeOutTime = .5;

Math.min(linear(time,inPoint,inPoint + fadeInTime,0,100),linear(time,outPoint - fadeOutTime,outPoint,100,0))

If you're not sure how to do it, here's a tut on that:

https://bluefx.net/how-to-add-opacity-to-layers-footage-after-effects
Hope this helps

http://bluefx.net