Hi MsBinky,
Not trying to be a smarta*&...but welcome to the world of wildlife rehab. This is an example of what Animal Planet doesn't show you on their "feel good" people saving wildlife stories. This is most likely one of those cases that I have ever so often when you do everything correct but lose the animal. And it happens....and it happens quite a bit. It is most likely nothing you have done wrong since the other is healthy....but seriously, that shows just how delicate these guys are. It has happened to me just like that....the day of release. I remember one little guy....came in a litter that was only a day or two old....and they all had to be tubed (I had to insert a feeding catheter and feed directly into the stomach). He was on his "hidey box" when I went outside to prepare the car to take the cage to the release point. I was outside no more than 5 minutes. When I came back in, he was on his side and died in a few minutes. So don't beat yourself up. Without you, he wouldn't have made it this far. You gave him the chance he most likely would not have had otherwise. It just didn't work this time.
As far as treatment to try to pull him thru....unless you have a sympathetic vet it will be difficult....and still will be if you have a vet's help. Most likely what you see is that terrible gut conversion they get about 21 days old or so. It is a violent conversion of the pH in the GI in which the gut converts quickly to an adult acidic environment. The beneficial bacteria can't withstand the quick change and will start to die off. It is very similar to a condition called "cecal dysbiosis" in domestics. The good bacteria will be overtaken by toxic bacteria such as E Coli and Clostridium. The prognosis is very grim. I have managed to pull a few thru by heating their body temp up to the high range of normal, hydration by SQ at 10% of body weight (WARNING-->for those of you that can administer SQ...this is way above the proper dosing) and administer a drug called Metronidazole (Flagyl) at20 mg/kg PO BID (I wrote it like that just in case a vet will help and there will no question on dosing). That drug will most likely need to be compounded since most vets only carry the tabs but there is a suspension available. It tastes really nasty. Not trying to be gloom and doom but most of the time they don't make it very long once they roll. It is not a pretty sight to watch this and you will most likely hear a shrill scream at the end.
I can assure you that all rehabbers have been thru that. There is a huge learning curve and rest assured, I lost a lot of animals when I first started. And don't think I don't lose some now because I do. There is only so much we can do from the medical end. But even though you feel this is bad, and it is...don't think of it as a failure. If he doesn't make, that bun's life had meaning....first, because you cared enough to help him in his hour of need....and second, you have learned valuable lessons that can be applied should you find more cottontails later on.
There is a little trick I use and it seems to work quite well. I use Oxbow Critical Care starting as soon as they eat solid food. It's in their formual initially and I start out with a very small amount about day 10 and work an increasing amount into their food....I even sprinkle it on their greens and have had some that would eat the CC on their own....that was nice. You hear of many people using acidophilus too....and it's usually lactobacillus. Well, that doesn't grow naturally in a rabbit's gut but it does seem to work. It works by acidifying the gut....look at the first four letters...acid. Bascially what I have learned over the years is how to manually manipulate the pH and control the gut conversion. I start the change in pH a little earlier and even out the conversion and it seems to work quite well. I am also seeing some benefit in using lactobacillus casei. Still working on that one.
Good luck...and I will be checking back often...send me a PM if you need more info.
Randy