Huge flat worm issue

[scott_r]

I've been about 1 1/2 years in the hobby here and things were going great till I noticed all this rusty colored specks on my sand bed and rock. I left it for a while and it got really bad and thought to google it and see what it was....UGHHHH was it a wake up.
So I go to the LFS and he sells me a product called "Flatworm Solution" tells me to double the dose, buy some carbon and all would be good. Well things went bad...really bad.
The chemical killed some flat worms which I siphoned out. I ran lots of carbon in my canister filter. I cleaned the filter out 1x after about 2 hours of sucking up these poisonous bugs. I changed maybe about 1/10th of my water.
Immediately all my sps and zoas closed and white slime appeared all over my rock. My tang went crazy and died 2 days later as did my Fuzzy Dwarf Lionfish. My 2 Blood Red Fire Shrimp lost their whiskers and look crippled now and color is washed out.
Its now been over a week and all coral/zoa/mushrooms have bounced back and look good but I still have some of these worms. Im wondering whats the natural way I can get rid of the most possible then possible do a proper kill off with a chemical. I know I didnt get enough water out of the tank..my fault and these worms poison took its toll.
Can I take out my rock and treat it, then do a siphon then a kill off? What the best way to clean your rock? Im hoping to not see dead livestock again...I hate these red worms.

Cheers!!