I'm not being a wise-guy when I ask the following; I'm just trying to understand :)
I've had his filter in the tank before I even got him (I was cycling before adding any fish). When changing the layers of his filter, I do so alternately, rinsing the new layer in his old water. His filter is still in the tank, I just turned it off a few days ago so as not to potentially add to any difficulty he may have swimming. Yet, you think that turning off his filter will cause the beneficial bacteria to disappear?
Sorry for the vagueness of the food portion. I use the NLS small fish formula, which I'm sure you know is really teeny tiny. I say smidgeon because I use less than a pinch, which works out to be about 5-9 pellets or the equivalent of 2-3 pellets of the typical size most feed their Bettas.
His poop has always been brownish/copperish/reddish, usually bun-style, sometimes a chunky'ish log.
Thor is not fuzzy (and his water is not cloudy), no white spots, no gold specs, no bulging eyes, no pine coning.
Have you tested your water? If so, what are the following parameters?