When I soaked them the other day I used 35% peroxide and used 10ml to 3 gallons. Should I also just pull off all the brown roots
Yeah. Take as many of the damaged roots off as you can. If you can lift the top away from the nutes it's better so you aren't dropping any in the nutes. Use a strainer to get any bits out then dose it good with 35% peroxide at about 4mls/L/qt every 24 hours. If you get 29% like the last gal I got increase the dose to 5mls/L.
3 days ought to kill everything off then do the same 36 - 48 hours later. The 36 would probably be better. New, white roots should be starting by then or shortly after.
Keep up a maintenance dose of 0.5ml/L twice a week and keep a sharp eye out in case it returns then a good shot should knock it back.
Almost forgot. Mix up a liter at the 4 or 5ml/L dose and pour it thru the net pots getting everything wet with it to kill off anything in them. Don't worry about the roots in the pots. Those are tough but because new roots may sprout near the bottom of the net pots or on the sides a bit of water poured thru 5 or 10 min later will help protect them.
You should be able to beat this.
Good luck!