Well since my tank has been up and running since Novemeber my L/S has settled to about 1 1/2 inches thick on the bottom and lately I noticed I've had a problem with cyano and diatoms growing on the substrate. Yesterday I added another 17lbs. of L/S and 6 nassarius elephant nose snails. I slowly mixed the L/S in with my fingers. I'm a little nervous hoping it doesn't have any detrimental affects on the bacteria in the old substrate.

there wouldn't have been much if any denitifying bacteria in there, however a few extra water changes and running some carbon, might not be a bad idea

Since Sunday everything looks great, no algae present anywhere. I also ordered the Rio 6 pump with some loc line.

Because your in a nano situation, your ideally keeping inputs low & maximising outputs, so the bacterial armies chewing the load within the tank should'nt be reproducing like mad in an effort to assimulate excess.
Now compound that with the time it takes to make a bed bio-logicly active & benifical . You did said NOV, giving four months so you should be nearing the maximised mark over the next month or so, adding new media adds to the flavour & that to will be new real estate to cover. all in all it sounds like its doing ok

I believe I didn't have enough sand in the beginning so now I should be up to par.
The nass snails are doing a great job turning over the sand. I should be receiving the Rio 6 pump today, so I'l be upgrading the flow and also adding some locline with two heads, one pointing towards the surface and the other facing the right side of the tank in the along the backwall. This should be my last upgrade to the tank I imagine So far I've added the nanotuners 4.36 lighting upgrade, modified the flow from 1st to 2nd chamber, sapphire skimmer in 2nd chamber with Purigen bag, L/R rubble in bottom of 2nd chamber, Chemi Pure elite bag in 3rd chamber with a few pieces of L/R rubble, heater in 1st chamber.

Current stock:

Candy Coral, Zoas, 3 Xenias, 4 small featherdusters, Green Leather, Green BTA, star polyps, Firefish, 6-line wrasse, saddleback clown, cleaner shrimp, emerald crab, Pom Pom Crab, 7 nassarius snails, 3 cerith snails.