Another thing is the water was clear with a yellow tint to it when I first mixed it. Now it is more of a white cloudy appearance (from so much ph down?).

My pump is running 1.3 quarts a minute continuously. What off on time would you suggest? I've never used a timer on a pump so I'd guess at 15 min on 2 hrs off?

Would you also suggest switching medium? I'm going to order some in a few days and was looking at switching to try something else out

I run my pump for 20 minutes with two and a half hours off which seems to cater for those plants that don't like over watering plus it allows the plants to take a deep breath until the next cycle with no bad side effects. At night I do not use the pump at all so after 6.30 pm until 8am there is no watering again with no side effects to the plant.PS if you use rockwool with regular watering this can cause problems I use expanded clay which still has sufficient wicking properties to keep the plants happy.

I don't have experience with using a timer either. I have a NFT system but it's a vertical tower so the rockwool doesn't sit in the water.

I saw something similar when I started doing deep water culture. My roots would brown and eventually get a slime on them. Also my water would get cloudy and then get some jelly like slime in the water. In my situation I started using beneficial bacteria in the water. My problems went away completely. If your situation is similar to mine, then you may want to get a small bottle of Hydroguard or Orca mycorrhizae. There are probably 10 or so similar products out there that do the same thing, but these are the only two that I have personally tried. Both worked great, so go with what is cheaper or easier for you to get. Test a small bottle of it. If it solves your problem, then you can get more. If not, then you're not out much.