I wonder about treating your yard with food grade Diatomaceous Earth as well as sprinkling some on Franklin's greens (although if you treat your yard he would naturally eat some.) I just did a quick search and found this in regards to horses and bot flies... http://ezinearticles.com/?Whats-the-Buzz-About-Bots?&id=5632003
Just your regular fly spray can (usually) control bot flies around horses, so I'm wondering if it can be used on a tort. Might be a little bit easier and possibly cheaper.
Bot flies are horrible! I'm assuming their life cycle on any animal is the same as what they do with an equine host. Since they lay eggs on the horse's coat (legs and belly area), the horse then tries to groom itself (they are itchy) and licks them off, where they sit in the horse's stomach for nearly 8 months (!), then travel though the digestive tract and burrow into the ground to mature into adulthood.
The eggs are normally a bright orange color, and they are laid in clumps, so I would hope they should be easier to spot on a tortoise (no hair! haha). Bot flies normally lay their eggs around late spring and well into the fall, but I'm sure it could vary from region to region.
My horse is very sensitive to all species of flies and fly sprays, so I use an all natural fly spray made primarily out of Avon Skin So Soft...I wonder if you could mist a tortoise with it? You can also find a ton of recipes for it online, or even buy an all natural spray from a feed or tack store if you choose to go this route.