What should I scrub the rocks with? And should I use saltwater or ro/di water? One rock at a time is what I'm going to do, gonna take this slow and try to minimize stress for the fish. I haven't tested phosphates in a long time so yes most likely phosphates but its also nitrates.Leave tidal going and use for mechanical filtration-you'll need it. Plus it's good for water movement.
You can place a bag of chemi-pure elite in there. Sounds like you have a phosphate problem.
Post some of your parameters that'll help us help you. Test.
Not believing in rip cleans, whatever they are remove 3 gallons of water into a 5 gallon bucket and scrub vigorously each rock you feel comfortable with.
Rinse and shake, put it back in the tank.
You're going to have to work at this but it's always fixable.
Keep up on water changes.
Joel