Looks like the light is too intense. You can lift the light up to reduce the intensity. The algae are black beard algae or staghorn. You'll have to manually remove them.
Have you noticed any plants with black, slimy, stinky roots? Maybe you can look through the glass at any roots growing on the edge of the aquarium, or gently pull one plant up a bit to check. From your pictures at least I can see some healthy roots. You could also do some more periodic poking if you're worried. But sounds like things are not extreme enough to warrant tearing down everything.Is there anyway to determine whether using Equilibrium has ruined the substrate?
The Equilibrium will not ruin the substrate once you stop adding it. The sulfates will gradually be removed by water changes and H2S gas released from the substrate. Since yours is an established tank, it's possible that you are making the substrate too aerobic by unnecessary poking. The gas bubbles could easily be CO2.Thank you Mr. Green. I have reduced the lighting somewhat by adding a layer of black window screen .
Is there anyway to determine whether using Equilibrium has ruined the substrate?. i tried to determine if there is alot of hydrogen sulfide gas in the substrate by poking it 15 times with thin stick. Doing so produced 2-3 bubbles in 3 locations. Doesn't seem like a lot but maybe my method is useless.
If I need to tear the tank down and start with a new substrate, I need to do it soon, before it gets too cold in Maine to ship plants.