If the filter has a UV light, that should eliminate any algae problem.
Don't really know what you mean by 12 vs. 24 hours---are you talking about the cover?
So the cover is really for protection? It's too bad some kind of predator fence/barrier couldn't be put around the pond. I can understand why you would want to have it on at night with those critters around, though.
Some turtles are shyer than others (depends on the turtle). The fact that he's covered a lot(?) of the time could also make him more leery of any movement when he sees it. (He doesn't get a chance to learn to recognize you because he doesn't really see you.)
For pellets, the amount you mentioned is correct, every other day. He needs to have a varied diet, though. Adding some aquatic plants to the pond would be good. Look at the feeding forum for some other foods you can give. Some basil is OK, don't know about the other plants. If you're concerned about the possibility of your turtle eating poisonous plants, take a look at
http://www.chelonia.org/Articles/plantsthatpoison.htm
"You become responsible, forever, for what you have tamed." -Antoine de Saint Exupery-