Algae happens and is part of a healthy ecosystem. With a combination of manual removal and time it will go away. The red carpet like algae is most likely cyanobacteria -- also harmless unless it literally grows over your corals. Up the flow, turkey baster it (that's now a word), and manually remove it.
I'm glad things have turned around for you. Nutrients are important for corals, and way too often I see tanks that are p04 starved having the worst paling.
Personally long ago I had paling and couldn't fix it. I kept dosing no3 and it just wasn't fixing it.. Then I decided to try something everyone told me not to do -- Dosing phosphates helped tremendously.