The taint was removed (replaced) by the Fox, who appeared as Sakushi in Truth and Beauty. Yoshi spent the run dazzled by the Fox, then settled in to a Fox-touched personality. Hiro took advantage of the opportunity to get Yoshi to update his wardrobe and get a makeover. Master Zhou, already preparing to help Yoshi purge the spider taint, whisked Yoshi off to see Master Kwan, who, with Tara Shien, led Yoshi through a cleansing meditation that allowed him to shed unwanted influences on his personality.
As of Phoenix Hearth, he is untainted (though slightly Foxier than before and better-dressed) -- until he hits another Great Spirit with "Why do you do this?"
In The Eighth Name Yoshi gets covered in a double dose of spider goo, which apparently requires spiritual healing to remediate, rather than just soap and water.