It sounds like you don't have enough air running through the stones. They do clog, but you shouldn't have to clean them every night.
you could run them without a stone. Others on the site have used soaker hose effectively. Another option is to make an air lift to create a waterfall for aeration. basically float an inverted L shape of pvc on a piece of styrofoam. attach the end of the air tube to the bottom of the pvc pipe (It'll be submerged) the bubbles lifting will push water up and it will come out the horizontal piece and fall back into the water. search this forum for both aeration and air lift. you should be able to find pictures on the first page or two.

Thanks grizzman,

My Air Pump is a "60 Gallon tank", silent run type. I am running without the stones for now. I dont know if it is "as effective" as using stones but I am seeing very nice root growth for the time being.

I just noticed you had it split to three seperate stones. that means less air per stone.
I think the primary way to infuse air into the water isn't the bubble size but the amount of disruption at the surface. That's why waterfalls make such good aerators.

I agree the air lift design works very well, as well as the disruption on the water surface infuses quite a bit of dissolved oxygen into the water. But the air lift design dosen't work on falling water alone, the water is typically raised by many tiny air bubbles that churn, and mix the air with the water as it rises. So it really combines the best use of air bubbles (churning with a column of water), as well as surface disruption from falling water. Quite efficient.

Thanks guys. I'll have to do my research on that design. The single 6" stone in the main tank does did not get nearly as clogged up as the two smaller stones I had at the top of the NFT channels. I truly like the idea of bubbling the water as it goes through my system.

Here is a link that might be useful: The original setup