Adding some Z-lift will take care of the rapids during a layer if you are using 1.1.5. (Before this, during a rapid, the Z would lift, then come back down, THEN the rapid move would take place. In 1.1.5, S3D fixed this so that the Z lifts, the rapid move happens, then the Z comes back down.) Maybe 0.2 to 0.5 mm is all you need. One downside to this is that the Z-axis moves are fairly slow, and the lift takes place regardless of the length of the rapid, so it adds some time to you print.
(A I think about it, it would be nice if there were a threshold on the length of the rapid that would trigger Z-lift.......more than, say, 5 or 10 mm, perhaps, would be a good trigger point. Or maybe it's there and I just didn't notice it......)
But adding Z-lift will not be a total solution until at least 1.1.6 --- I observed and reported an issue where, when going from one layer to the next (with no Z lift), the rapid move occurs before the Z indexes up to the next layer height. I suggested the layer-to-layer Z index take place BEFORE the rapid X/Y to avoid CLONKing the part. And the layer-to-layer rapid, for the part I'm tweaking now, is quite often more than half the length of the bed!
For now, it might be worth it to just once try adding the Z-lift for rapids (and maybe some retraction and/or coast to avoid blobbing during the lift) and see if that helps.