with regards to the water testing...i'm doing it exactly as you described... for amonia the colour is bright yellow, Nitrate is bright yellow, Nitrite is bright light blue, and PH is a blue colour. - using API master test kit.
Hi, if I am remembering right then a PH of 7.8 and a colour of blue is the max that the standard PH test in the API Master Test Kit can test for.
You should also have a "High Ph" test, which uses a card with shades of orangey/brown on it. It might be worth running that test as well, as you Ph might be considerably above 7.8, but you don't see it.
Unless of course you are already using the high Ph test kit, in which case I've got the colour cards the wrong way around in my head, but either way, anytime I get a ph result in the 7 -8 range I do BOTH Ph tests, (high and standard), so it might be worth you doing.
Looking at your photos and your gravel though I'm almost inclined to think it is gravel dust. You say you let the gravel soak for several days, 'changing the water often' but in my experience this doesn't remove the dust from it. The dust in gravel is so fine, the only way I have found to wash it is literally have a bucket full of water, half full of gravel, and then lift a handful at a time, (with your hand!), through the water swirling it as you go, then placing it into a new bucket. When you've done the half bucket of gravel, you dump the water, (and all the silt thats washed off the gravel), and repeat with the next half bucket.
It still won't be totally clean, but it does a pretty good job. I would guess you've actually ended up with quite a lot of silt in with your gravel. When you do a gravel vac is the water that comes out milkier than that in the tank would you say? (Can be very diffifult to tell as the tank is lit, and obviously is easier to see through). You can check by gravel vac-ing into a bucket, and then take a drinking glass of water from the bucket, and look through it to compare.