So now that I have a path forward on those issues any suggestions on the brown stuff growing on rocks an the cloudiness (or will changing lighting out and more floating plants and the timer fix that)?
Probably. I do think the light is on too long, and reducing that plus some floating plants will or should result in clearer water. And the algae will be hampered. What you look for in situations like here is not the algae disappearing, but not increasing. Once you have things balanced for that, removing the existing algae can be considered. I tend to leave it on wood and such, but plant leaves can sometimes be cut off if there is evidence of new leaf growth free of algae.