Bec, that's good news, I'm glad they at least have a fair chance to recover. I looked at the link you posted, that looks like an excellent source of info. I have a couple of comments and suggestions, though.
If your birds aren't showing swelling, I wouldn't give the prednisone. Even if they are, (now this is just my preference, if you feel you really need to use prednisone, then do so, and I hope all goes well) I would opt for an herbal instead, such as homeopathic arnica. My reason for this is that arnica is extremely effective, and homeopathic treatments (homeopathy using extremely tiny amounts of whatever active substance they're made with, to trigger the bodies own healing processes. They work amazingly well.) don't cause side effects. Prednisone can be some nasty stuff, and I wouldn't want it in my meat birds that I'm planning to eat later. When stopping prednisone, there can be severe rebound swelling, which is why you're supposed to taper it off, slowly. Arnica won't do that. Also, I don't know how long you'd have to wait to let the prednisone clear out of the bird's systems, but arnica could be given through th entire life if the bird, and still not pose a hazard from eating the bird later.
Also, the prednisone was recommended for silkies that had brain injuries, (because of the holes in their heads) I don't think yours did, so it may not be needed, anyway.
The rest of the treatment sounds good, though, I'm thinking it could work. I hope so, anyway.
As far as a mold or botulism, I think they'd be more likely to encounter that indoors, possibly in bedding, or in the feed. It's possible they got into something outdoors, but not as likely.
Vinegar kills mold and fungus, as well as a variety of bacteria, and won't hurt your birds. If you scrub the suspect areas down with vinegar, you'll probably get rid of the culprit, unless it's in the feed or bedding. A little apple cider vinegar in their water, wouldn't hurt, either. I'd use organic ACV, and if possible, one that contains "the mother", which is the live, active culture that makes the apple cider become vinegar. The less expensive, ordinary distilled white vinegar is fine for the cleaning, though, I wouldn't use the organic stuff to scrub a wall. You could even just spray it on the walls and floor, before putting down fresh bedding, if you don't see any visible mold or anything.
I'm getting over an illness caused by mold, myself. I have an allergy to molds. so I have to watch it. I have OSA, (obstructive sleep apnea) and use a machine called a CPAP (continuous positive airway pressure) at night in order to breathe properly while sleeping. Anyway, I neglected to clean the water reservoir as often as I should have, and a little mold began to grow in it. (I know better, I just got busy and forgot to do it) I have a spare, and I'm stopped using the machine until I get this thing cleared up. I became very ill, but I'm treating it with herbs and essential oils, and I'm much better today than yesterday, and yesterday was much better than the day before. I'm using oils of oregano, cinnamon, and Moroccan blue chamomile, and doing saline irrigation to clear anything from the sinus passages. Not something you can do with a chicken, but just to show there are alternative treatments for a lot of things.
Best of luck, I'll be waiting to see what happens.
Still not heard from the vet (which I think is good news in that it's not ND). However, after Blue 90292 suggested looking at the disease page (doh!), I did and after some searching found someone else who had had what sounded and looked like from the photos exactly what my chicks are suffering from. 
