Joel-
I didn't have to do as much rock as you're going to have too, but I did acid bath my rocks for my 28 gallon before starting it up again to remove all the green hair algae I was dealing with. I went and bought Muriatic Acid from home depot and used the recommended dosage instructions that I found on RC. Let me tell you, this is by far the best way to get rid of the algae. Bleach was ruled out because there is always a chance for bleach to be leeched back into the tank. The acid on the other hand dilutes pretty well with water, hence why you can use it in pools. I put water and a full bottle of acid into a big rubbermaid container and put the rocks in one by one wearing chemical proof gloves obviously. I then had a second tub that was just water with the hose constantly running into the container to always have fresh water. Once the acid stopped bubbling, I put the hose into that container and ran fresh water to dilute the acid. Let this run for like 20 mins and just let the water overflow the sides of the container (I did this outside on concrete). Once I could put my hands in the container, I took out the rock and then rinsed them in the 2nd tub and left them out to air dry. The difference was night and day. I'll attach some before and after pictures. Remember that if you do this, the rock will be dead and you will have to reseed your tank.
Matt
The acid I used:
http://www.homedepot.com/p/Smart-2x1-Gallon-Muriatic-Acid-2118-HD/100119310
Picture before: Notice the rock in the upper left hand corner was covered with algae.
http://s232.photobucket.com/user/saltnewbie/media/New 28 Nano/P1010045.jpg.html?o=6
During:
http://s232.photobucket.com/user/saltnewbie/media/New 28 Nano/P1010050.jpg.html?o=8
After: So much cleaner
http://s232.photobucket.com/user/saltnewbie/media/New 28 Nano/P1010051.jpg.html?o=5
So far it's been 8 months after doing this and my tank has had no algae return.