Hi Kirsten
I know how hard this is on you and Luna.
I was wondering if you could put Luna(your older original kitty) in your bedroom.

Luna deserves to have you all to herself for a while.
She's older and now with the weight issues and maybe some depression.
not as quick to get back at her younger sister,it may help Luna's self worth and it will remind
her of how important she is to you.
making her the Queen.

Or better yet,only at night when it's time for bed,bring Luna in.
i know Lilly will protest but after awhile the noise outside the bedroom will quiet down.
(we had to do that on different occasions)

litter boxes and water bowls in both areas are a pain but i think it may help.

If this is not a good idea,i still am thinking of another.

or...how about a spray bottle for Lily when she acts on Luna.
Spraying Lily every time she starts to pounce on poor Luna.