Race issue: not quite sure what you mean, but are you using several race/hair/eyes mods at the same time? Cause you can use only one, cause they conflict with each other. You could use Wrye Bash in such case I hear, don't use it myself, but I believe you can use the CS to fuse the mods into one.
Potions: In the object window, just open the Potion tab and right-click on any potion and select New. When you made your potions, look for vendor chests in the container tab, edit one by emptying it and adding the objects you want your merchant to sell, and make a new ID form for it. Place that chest in the cell and edit the stats on that chest, to make it's ownership that of your merchant. That was what you were asking, right?
Skooma Den: I'm not sure about this, since I haven't added buildings myself. But I assume you can just use a static house in the architecture tab, and in the worst case, building it wall by wall, but a shack shouldn't take too long. Then just copy the skooma den cell, and delete the people etc. And refer the door in the cell to the door of the new shack outside in the waterfront.
EDIT: Oh and btw, in order to keep the vendor chest safe from thiefs (you), place it somewhere outside of the walls, where you can't reach it without toggling off collision.