I definitely say get rid of the calcium sand, that stuff isn't good for bearded dragons at all. Also, if your dragon is less than 14" much higher risk of impaction from ingested sand. If you really want a sand substrate, once he is 14" you can switch him to washed and sifted children's playsand. It is safer by far than any calcium based sands.
Dust from the sand, or the sand itself certainly could be causing the problem with his eye. Get rid of the calcium sand, switch to just plain paper towel. If you don't notice an improvement in the eye..in a few days, take it to a vet to flush out the sand or whatever else may be causing it. Waiting too long could mean damage to the eye and/or infection.
The basking spot is rather close to the bulb..6" doesn't give much room and you don't want your dragon to get in contact with the hot bulb at all. (unless there is a screen or something between the dragon and the hot bulb). Are you sure the basking temps are good? Sometimes it is easier to just use a higher watt bulb and move the basking spot lower, than having the dragon dangerously close to the bulb. You can just use regular household bulbs for basking lights, don't need to get the more expensive petstore ones. I don't find any difference between using a $.50 house hold 75 watt bulb to the $5 pet store one. The cheaper one may burn out a bit faster...but I rather spend $.50 a year then $5 every two years...(assuming the pet store bulbs actually do last two years...never used them at all).
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PHLdyPayne