I'd say they aren't completely over the fungus. I don't know if a cow is the same as human, but humans with an alkaline gut ph is between 7.0 and 7.5 . Virus, fungus and bacteria cannot live in an alkaline environment. You need the cow's gut to be alkaline, so what do you give them for bloat? Over here, the cheapest thing is sodium bicarbonate (called baking soda here). Alkanize their gut ph and then give them probiotics to get the good bacteria going again.
Also, I'd raise the magnesium, zinc and iodine in your mineral program. I don't know about Africa but over here 70% of Americans are magnesium and iodine deficient so that means its not in the soils nor in our food and if I'm not getting it, then I seriously doubt that our cows are. Iodine has antibiotic properties to it, zinc reduces the arthritis (which should help because I wonder if the cows are standing in the water because of reduced oxygen to the blood cells and the feet aren't getting the oxygen they need plus maybe a slight temp?) and magnesium has so much stuff its needed for we've have to start a new thread just for it.
Here's a link and one vet's recommendation:
http://www.mindfully.org/Health/FMD-Homoepathy.htm this may be easier to obtain sodium tetraborate (known as mule team borax over here).
Please do your own diligent research as this is just my suggestion only. I would never intentionally misguide someone and we don't have FMD over here................. yet. I'm sure we're in for all kinds of surprises over the next 5 years. I have used borax 1/2 to 1 cup in 100 gallons of water and it clears up snotty noses and coughs. I have never used it beyond 3 days straight though and they need at least 3 days off per 7 days (this is important so don't give it every day).
Also you can use it on crops, 1/8 to 1/4 tsp per one liter of water.
You need to eradicate the fungus, then work on getting oxygen back into the cow's body. Just remember fungus (like cancer) lives on fermentation and sugar. When you get the oxygen levels up, your cows won't be standing in the water (stop and think about it, a foundered horse has problem with his feet because he isn't getting oxygen to the blood cells in his feet and the blood cells are dying off) .
Can you get food grade hydrogen peroxide?