Thanks for elaborating. I was trying to point out to you that you seem to have omitted alot of information in previous posts, and you have certainly made somewhat contradictory statements in the past. Good for you for not losing your temper.
In a situation like this I think that its very important to be as thorough and direct (yes, honest) as possible: that way you can get (hopefully) the best advice. You have a BIG problem on your hands, so please don't spare the details.
I'm not trying to hurl insults at you, or anything like that at all, but rather, I'm trying to extract as much information as possible from you, to better evaluate your situation.
That having been said, I'll try answering some of your questions.
In the wild, free-roaming turtles would probably not congregate, and remain, in small areas (the size of your enclosure, say) for any significant length of time, so diseases would probably not spread at such a rapid rate. Their water source would probably be flowing water or a pond with its own ecosystem/biological filter in place. Their waste would be dispersed, rather than concentrated in small areas.
I have not come across any literature about respiratory diseases in wild box turtle populations and how the wild animals cope should they become ill, but that does not mean that any such literature does not exist. They may simply crawl away and die. It has been stated that, overall, wild box turtle are relatively healthy, but then again, we only see the survivors.
About soil sterilization: there is a very simple technique used by gardeners that entails laying black sheet plastic out on the soil surface for a certain period of time: enough heat builds underneath to kill weed seeds and an assortment of pathogens. I don't know if it would work in your situation, but I'd certainly give it a try, since it is so low-tech.
As for your pond, scrubbing it out with a bleach solution will certainly work: from there you need to check out filtration options, and evaluate whether or not your pump is adequate for the size of your pond: a general guideline is that a pump should be powerful enough to run the capacity of your pond through it in an hour. In other words, if your pond holds 100 gallons of water, your pump should run 100 gallons per hour. Up to a point (you don't need a pump to shoot water across your backyard) stronger is better. Our pond holds about 100 gallons: our pump is a 250 gph pump.
There are alot of filtration system options out there, so you'll need to check out different options: see if there's anyone in your area who does ornamental ponds, or who has experience with koi ponds: koi require near perfect filtrations, so someone who has experience with them will know their stuff. Many aquatic plants are perennial, so you can leave them in the pond over the winter. Others are tropical/annual, but the good oxygenators are also inexpensive, so replacing them annually is not a wallet-buster. The plants are important for filtering water.
As far as keeping better track of your turtles is concerned, consider this: if you check them regularly, you can better monitor their overall condition, and be better equipped to nip a problem in the bud before it spreads. If you keep better track of them, and are more observant, you will become better at spotting changes in behavior, etc., that might indicate a problem. Symptoms can be very discreet, and if you don't know what to look for, you'll miss it.
More food for thought.
Stephanie