Toadstools are pretty hardy corals. My guess is that it's stressed from the water quality issues. Although water changes are the best thing to do when you are having a water problem, the water changes themselves can be stressful to the animals also.
I would not move it to the quarantine tank just yet. Your water parameters from today are looking good (much better than before). Because toadstools are usually pretty resilient to stuff, I'd wait it out and see if it gets better over the next several days.
What do the spots look like? Does it look like the flesh is dead or rotting? If so, you can cut out the dead/dying areas with a razor blade so that only healthy flesh is left.
Toadstools are a type of leather, and leathers periodically shed their outermost layer. During this time, they tend to wilt and look unhealthy, and crap starts coming off of them. This is normal though. Are you sure it's not just shedding?
