Thanks for those points, I think Im on the right track. I now have files in AE using Alphas.
Im a bit embarrassed by not getting this to work, but may as well show my workings.

The fluid seems to be rendering fine in maya, but when brought in to AE they are more opaque. I did mess a bit with the transparency of the fluid as you said, but should it not be accurate in the Maya render? Also there is a Linear workflow in place.

cheers.