The diet has already been posted. Are you feeding the Timothy Complete with or without the alfalfa? I would also recommend dropping the yogurt treats (for sure), but I would recommend gradually switching away from the Timothy Complete to another pellet from a different manufacturer. I had a long-term problem with mushy poop with all 5 of mine, and since we've reduced the Timothy Complete, the poos have been a lot better. I would also drop the cilantro, as I've found with mine that anything with a soft, quickly wilted leaf like cilantro exacerbates poopy butt. Kale can also be gas-producing, which can cause poopy butt as well. Try more fibrous herbs, such as Italian parsley, dandelion leaves, romaine or escarole lettuce, thyme, dill, oregano. Lots of people swear by plantain leaves (the weed, not the banana-like plantain!) and strawberry/raspberry/blackberry leaves for regulating the gut in rabbits. Some people like Sherwood Forest pellets (alfalfa, timothy, flax and some vitamins) because they contain no soy or wheat to upset tummies, but mine responded badly to either the alfalfa or the higher fat content (5%) in these pellets. It's worth a try though (very small amounts to start with).
Intestinal disorders can also be due to some chronic and low-level disease or pain going on -- if he has had e.c., the parasite may be becoming more active again as he gets older. Have you tried some pain meds for a few days to see if that helps him? You could also try changing the water on the off chance it has high levels of something that is causing an imbalance -- minerals or bacteria or other contaminants. You don't mention what specifically you've tried changing, so I don't know if you've already tried that.
Parasites might still be the problem -- one negative fecal won't tell much since most parasites shed intermittently. You could do some repeat fecal tests at intervals of a few days, but for parasites, I would expect the poopy butt to be more cyclical and intermittent, not constant. Has he had any stasis episodes along the way, or abdominal pain, or is it just the poopy butt?