Perhaps something in that new rock was decaying, and is adding to the ammonia level.

Leather corals shed, that is normal. You can siphon it out with a turkey baster or some tubing.

Caulerpa, depending on the type, can die off in your tank. If it releases the green liquid within its stems and turns clear, it has died and will dissolve away in the system within 48 to 72 hours. I would remove it as soon as I noted it was clear. Certain types don't do this if they are under a light 24 hours a day, such as in a refugium.

Your tank is suffering through a mini-cycle for now. Adding a detoxifier to the tank for now will help, and don't add any more livestock for at least 4 weeks. Water changes will help keep the level down, but remember ammonia is toxic to fish and inverts, as is nitrite.