If he's molting right now, that could be the cause of the gut slowdown and the small fecals. As long as he's still eating and pooping, you may be ok for now, but you will want to make some diet changes to see if there is some improvement. I would cut way back on pellets, don't feed any treats, sugars, carbs, grains, or starches. Green leafy veggies are ok, but avoid cruciferous veggies, including the ones that are leafy. And feed tons of grass hay. With you cutting back on the pellets he should eat lots more hay, which is what you want, and it should help the digestion move better and hopefully clear up this problem.
You may not need simethicone yet, if he isn't showing any signs of discomfort or pain, doesn't have a bloated belly at all, and he is still eating normally. You may want to be caustious with the probiotics as well. I use them with my rabbits at times, but once when first using it with one of my rabbits, it actually upset his stomach and caused a gut slowdown and small poops, which he hadn't had before. So now when I first start to give it to a rabbit, I start with a very small amount, smaller than the size of a pea, and gradually increase the amount, as long as it doesn't seem to cause or worsen the digestive problems. I use the Probios gel, but there are several other brands that you could use as well.
Not sure what you could use to replace the fleece with. Flooring is hard for rabbits cause the need something non slip, but then with chewers, you also need something chew resistant. Maybe try and provide lots of other things for him, that are safer to chew on.
