I have been trying to use a CTRL+F4 exported head to work as a new custom head and have finally got it to work in a fashion.

When I load the nif into the HeadForm it appears as it should be in the preview window but when I attach it to an actor things go wrong.

The eyes, hair and brow are not what show up in the head form, they are being replaced with the defaults.

The eyes are too high in the eye socket, the pupil is half under the upper eye lid and the upper lashes come out of the brow.
The brow is too far forward, they are floating in space in front of the forehead.

I have tried repositioning the eyes and brow in Nifskope but the changes do not reflect in the CK.
Changing the eye and brow type in the CK do not help.

There are no errors being generated when the nif is loaded in the CK.

did you create a .tri for your head?