If you have any questions, feel free to ask, I will gladly help. Setting up resorep is easier than it seems, and once done, you can use any texture mod. I'm still thinking on a more clear tutorial.
Resorep does not change the game, it is a directx hook that swaps the textures stored in the memory while the game runs with those you just chuck into a mod folder... Quite easy once it's set up, and poses no danger or anything.

UPDATE: Just to make sure you know: this mod works from the start, no need to buy any outfit, and once installed, it works with any kind of outfit, modded or original, as the hair, eye, and face textures are the same for all. Also works in cutscenes.

1.0 readme:

This mod finally lets you play with -Green eyes -brown hair -brown goatee. All of this three are selectable, though original blond hair would look crap with brown goatee XD

Current issues:
-Hell, Black Flag's lighting effects ARE optimized for a blond lad, I can tell you that... Dark hair looks a bit less shiny, and a tad sun-bleached. It still looks awesome, but yep- they had their reasons to go with a blond one. Still, I like the brown look.

-By the time I FINALLY found the balance between the red parts of the hair dds image and the neon parts of it, (if you fail, the whole hair disappears) I was able to create brown hair, but this removed all the 3d facial hair, save for some of it in a very close view... So I've got an almost clean shaven Edward... I left it as a feature XD if you prefer it...

-To counter this, I modified the face texture instead, and added a brown goatee- you can go with that, or with brown hair and shaven face. :P

-I also modified the eye color to green, but this is also some hard stuff, as the eye is originally absolutely grey, then the engine adds an odd blue hue, hence the blue eyes. So I had to produce a yellowish eye texture, to get a green one with that cursed blue hue in work. If anyone plans to add more eye colors, keep in mind that you have to count the extra strong blue effect when you modify the texture....

Installation:

In the zip file I included all useful combinations of the green eyes, brown goatee, and brown hair. Just select the one you like, (folder name tells you which one is which) and copy all .dds files from THAT folder to your RESOREP modded_textures_folder. (just the dds files, not any folder...) If you do not have Resorep, please continue reading...

Resorep installation:

Others written guides before me, but I made one as well, as straightforward as it can be in 7 easy steps:

https://www.nexusmods.com/assassinscreedivblackflag/mods/15

You can find all instructions there, but always feel free to comment and ask for help.