If the fish had swallowed a stone, it would be stuck in the throat & usu. unable to close its mouth. If the fish is eating, this is unlikely.
If you felt the skin (the slime coat is on top of it) and it felt normal, then the slime coat prob is.
That is a small tank for shubunkins ... although they are smaller than comets or commons, they do get big (8") and yes, they are best kept in ponds. I would suggest testing your water parameters. It is likely that the water quality had deteriorated, bringing on the illness.
QT of a sick fish is always a good idea, although if it is a water quality problem, you need to fix the water. ( ....water changes for start ....) Eventually you would need to consider a much bigger tank or rehoming the fish.
Long thin clear poop with a red anal vent is indicative of an internal infection, prob bacterial. Parasites are possible but less likely. Before treating this, you do need to make sure the water quality is good. Medications will not help in the face of poor water.
If the fish is not improved with clean water, then a course of medicated food (eg MediGold .... basically anything with kanamycin) is worth trying. <Depending on where you live if medicated food is available over the counter .... Eg in EU countries, you need a vet prescription to use antibiotics.>