Nutscaves was already highly contaminated before I took the three critical measures above. Dwarves walking over or handling contaminated items were falling ill left and right. People were dying with contaminants on their clothes, and the clothes would sit a while. Then I'd decide they were in the way, or need to build (or deconstruct) something where the clothes pile was...and somebody would touch them.
The trade depot was a particular problem area. The items would get moved or stepped on, and the plague spiral would start anew. Contaminants weren't just on the clothes and other gear, either. They had found their way onto building materials as well.
I had no idea what to do about this to begin with, so I started making people take off their clothes when I realized they were wearing bad clothes. This was the wrong step to take, but I didn't know it at the time. I believe the right step to take, if quarantining has failed and something contaminated has found its way into the fort, is to purge the contaminants, now. Naked people handling contaminated clothes just make the problem worse.
There are many ways to get the contaminants off of an object, and my favorite one is magma. Luckily I had found the magma sea before people started dying of plague. I designated a dump over the open magma and started dumping contaminated items: clothes, equipment, stone. It was a painstaking process and some of the dwarves taking the items down to the Magma Clothes “Washer” got sick. Others had to come to replace them. Eventually enough dwarves who happened to be wearing gloves and shoes were hauling, and we managed to get rid of the bad stuff.
Another washing method that is easier than that, is to wash in a dwarven bathtub. This is preferably a bathtub not a lot of people will be walking through. In my fort, the one in the second cavern pretty well never gets touched, so it doubles as a clothes washer. I just designate it as a dump and the dwarves will put the items in. When the items are reclaimed, all they'll have on them is "water covering". Just don't dare reclaim them until the filth has been cleaned from the tub area.
Another method I (accidentally) used to get rid of contaminated stone is, if I know the stone is contaminated, and I know I'll want to use that type of stone later and may have an accident with it if I forbid it--just (make sure all builders are wearing gloves and*) use up all the stone by building a floor with it. If it's used to build a floor, the floor will be contaminated and a dwarf will come along and clean it fairly promptly. As long as he doesn't stand right on that dirty square, he won't come in contact with the contaminants. They try not to stand on the dirty square when they clean, if there's only one such square. I cleaned the stone I didn't purge with magma, this way.
((* Note: I believe there is still some risk of contracting the plague when handling the contaminated material, but it's not 100% if hand protection is worn.))
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