It can take a week to adjust to any change, much less a new cage followed by a new plant.
I'm not sure what you mean by "cluttered" but chameleons like to be able to hide from you and lots of leaves are good for that. If it's so dense that he has trouble moving around, I would consider trimming the plant back a bit, but if it's just really full of leaves and he's able to cruise around the plant out of sight, that's likely to make him very, very comfortable.
I think you've just made big changes in his life in a very short time frame...he needs time to adjust.
Covering the soil with rocks will help prevent him accidentally swallowing dirt. Just make sure you get rocks that are big enough he can't possibly get one in his mouth. Places like Lowes and Home Depot have bins of various "ground cover" rocks you can buy by the pound. Get the biggest you think your pot can handle.