I'm sorry its taken me so long to comment on this thread. I know I commented on the other one you posted a long time ago but I've just been so wrapped up with my own troubles that I haven't even been reading other threads until today.
I really feel for you and have an idea what you're going through. Sadie had unexplained bouts of vomiting and diarrhea on and off for months (around 6 months).
After being on parasite medication (Panacur), bringing in multiple fecal samples and spending a fortune on blood work we still didn't know what was wrong with her, everything came back normal or inconclusive.
I eventually put her on a hypoallergenic dog food for close to a year, which calmed things down. She's never had the problem since.
Since Sadie and Bailey are two different dogs I can't really give you much advice, except go to a vet you trust and hang in there, try to stay positive (haha, that's funny coming from me!).
If you get stuck without any medication for diarrhea like on a weekend, Imodium (Loperamide) can be used to stop it temporarily (start with half). Dogs can also be given Gravol (Dimenhydrinate)for an upset tummy, I usually give 1/4 to 1/2.
Like I said, hypoallergenic vet food really helped Sadie, I just wish I'd trusted my vet and put my own feelings/prejudicies regarding vet food aside and tried it sooner. It took care of all her problems and Sadie loved the taste.
I can't hurt to try treating her for coccidia, even if it doesn't work that could at least rule it out.
I was sure that Sadie had Giardia and she was treated repeatedly for it without success.