Shew, lots going on here. I'd start by slowing down your feeding. Next I would do some bigger water changes and keep up with that.
Crushed coral isn't bad if you keep it clean but most people struggle with this. Not to mention it's hard on some inhabitants. Soft sugar like sand is better...
I've always heard 10% water changes weekly or %25 every two weeks. A lot of your water change schdule will depend on your load as mentioned. You'll just need to feel it out. Just remember, it's better to over do it than under do it.
Sounds like you've got the desire to get it under control so it's just work from this point on! Nothing that can't be fixed though...
Good luck and keep us posted.