Hello, I know I'm a new member here, but I do have some knowledge. I'd like to point out that I don't mean to come across as abrasive, I am just trying to get to the point and be helpful.
First, I read all 186 pages. I'm not sure if she's still around since this thread dates back to 2011, but severum mama seems very knowledgeable (not to say other members are not, because they are, but you definitely should have listened to severum mama more in the beginning of your tank build, specifically about dosing with ammonia).
The tank looks great in terms of aquascaping.
What you really need to do though is just let the tank sit for a month. Don't touch anything. Don't add any fish. Don't move the plants. Nothing.
Just check your parameters and do a 25% water change once a week.
It seems like you are having lots of trouble with this tank. The reason is because you keep changing things. The tank is an ecosystem. Every time you change something, you flock something else up.
About halfway through your thread, you added Co2 and your fish started dying. Do you know why? It's because Co2 decreases the pH level. That's why you woke up and lots of fish were dead.
You know what you're doing, but you're not being patient enough and thinking about all of the variables. Just let things simmer. Wait until Ruby gets better. Let the tank stabilize.
As for your algae, you can fix this easily. Don't reduce the amount of time your lights are on, but instead reduce the intensity of your lights. Take out a bulb or something. Also, there is no reason to have your lights go off in the middle of the day for one hour. That is just going to confuse the fish and flock up the photo period for your plants. Remember, Algae absorb all forms of light, so having the lights go off for an hour is actually doing your real plants and fish a disservice.
I would leave the lights on for 6 hours, with no 1 hour darkness. Dose the tank with an abundance of Excel, keep the Co2 going (watch the pH levels!!!!!! especially at night!) and don't add any trace elements to the tank.
Also, cut back on your fish feedings and siphon the gravel. There may just be too much bacteria/rotting food/poop/etc that the algae can live off of.
As I said, I really don't want to come across as rude or brash, but you need to just let things stabilize.
If you have the time, take out the rocks with the algae on them and clean them. Scrub them HARD in a bleach solution (50% bleach, 50% water). Then rinse them and let them soak in some water with dechlorinator. Then you can place them back in the tank, algae free.
I will keep checking your thread for updates, as I thoroughly did enjoy your thread. I hope everything works out for you and your fish. If you have any questions, you can feel free to ask. I will be starting a 90Gallon build thread in a couple months, and I hope you'll take part in my thread, as well.