Flagyl is specific for protozoal bugs, not worms or flukes. Protozoans are about the size of a bacteria, in which you could not see with the naked eye. But apparently Flagyl must be prescribed for C. Diff.
I had white specks appear following a round of diflucan which is an anti fungul... maybe the white specks are the result of the c. diff infection.
Staying on a probliotic would help, I wuould consider the enteric coated ones like dr. ohhira's formula and EPS from Jarrow and I heard that Culterelle is good.
I would also consider Colostrum from NOW ... to help the environment and you may want to consider some charcoal (slurry) you can buy it in bulk powder from tom harrelson or others. the charcoal will soak up toxins... this is probably the cause some of the side effects that you describe