On a hay only diet the poops should actually be much bigger then normal since they would be bulked up with extra fiber and likely more of them. It sounds like he may have gas, you can try giving him some infant gas drops, the dosage is about 0.3ml every 8-12 hours. If he doesn't seem better within about 24 hours though I would take him to the vet.
Why are you only feeding hay? Holding off on pellets should only be done for a short time, like a few days to see if added fiber helps the issue if he may have eaten something that upset his stomach. Since you know the issue was a parasite causing the wet poops then feeding hay only isn't going to do him any good. If he is still having wet poops it's likely do to the meds. Pellets make up for any nutrients the hay is lacking, so he may not be getting all the nutrients he needs if you aren't giving him his pellets.