Fighting over a litter box is rarely about the litter box. If you have one dominant female attacking the other one near the litter box, it's probably Top Kitty's way of saying, "Don't forget who's the boss." It might be time to intervene and set things straight.
Add two more litter boxes to the house. That way you have one litter box per cat plus an extra one. With so many options available, chances are Top Girl won't be standing ready to attack all the time, especially because she's unlikely to know which litter box is going to be used next. Put the litter boxes in different rooms of the house to allow both cats more space. If the fights are about establishing territory, multiplying the number of litter boxes should fix it.
Buy a closed litter box. This might not solve the behavior problem, but it will allow the weaker kitty to do her business in peace, without worrying that she's going to get attacked from the back or sides. Litter boxes that have a small flap door are even better, as they provide added protection.
Spay the girls if you haven't done so yet. The bad mood could be partly hormonal. As cats reach sexual maturity, they can become more aggressive and frustrated, especially if you don't allow them to mate. Why does that result in litter box attacks? Well, Top Kitty could be simply showing dominance -- "It's my litter box, go away!" -- or taking advantage of the fact that your other cat is distracted and a perfect target.
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