If you have Cyano, and it looks like you do, they are consuming some nitrate, which would give you an artificially low reading.
If you are using a gravel siphon, it will not provide enough suction to clean the crevices on the rocks, I just used 1/2" ID hose and stuck the end in all the little crevices I could reach as the water siphoned. I would end up with a bunch of crap in the bucket.
As an aside, I have the same tank and am also experiencing a cyano outbreak. My setup is about 3 months old and I think I've been feeding my 2 clowns too much, even though they are just on flake.