1. When you make a face, first reset the face, then adjust shape and tone. Also using matching face-body texture will be helpful. However, you cannot eliminate head-body tone difference and neck seams completely.
2. Hair mesh is static(they cannot be rigged with any skeleton), so long hairs will clip through body mesh, even vanilla hairs clip(pick 'pony tail', then set it longest, see how the hair clips through). No solution other than using wigs(then ears will disappear).
I did reset the face before I started adjusting, twice actually. And I know you will still have clipping even with vanilla hairs, what I'm saying is the clipping has got worse I'll try get more screen shots and you will see exactly what I'm talking about.
Quick question...
You say you are using a body replacer..But do you realize that NONE of the stock clothes and armor will work with said replacer?
There are Replacers for just about everything....search ....EVE, HGEC ,
there are ones for Stock, MMM,OOO Frans.....think this might help.
I'm not using none of the stock armours it's mods I've downloaded, it's http://http://www.tesnexus.com/downloads/file.php?id=18806 I'm using that goes through the neck.