If you feel you must make a cover, the best bet would be to use hardware cloth. If you use chicken wire, rodents would go through the holes, and raccoons can tear it up because its such a small gauge.
You could just drape it all in bird netting. It will keep out birds and coons wouldn't want to fool with it. If you're worried about snakes then you'll have to do something about the gaps in the walls. I'd say if that 6 foot fence closes in the whole yard then you don't have much to worry about I'd think.
As long as they are not bullfrogs, they can eat a tortoise! I have had toads in an enclosure before and everyone keeps to themselves. Unless of course you are paranoid about disease, etc.
Not sure what to cover it with billy wanted to say wow that's an awesome enclosure!!! I'd love to see more pics of what you've done and how you made it.
See if you can find out if there are raccoons in your area. Rodents could get through the gaps in the enclosure, anyway.
You can protect them by locking them up in a secure wood hide instead.
If you only need to protect against birds, you can use bird netting, but I have had trouble with small birds getting stuck under it.
However, I have also heard that you can string fishing line back and forth, perhaps a foot apart. Bird can see it, so avoid it.
Frame in the side with netting (or you can use the fishing line there too), then use fishing line on top (above your neck, obviously, lol).
Small birds can get through, which is fine. But larger birds like crows and predators, etc., can't.