Either we can search for obvious strings like X-Uber-* and try to scrub them one by one, or we can just nuke the caches for all the domains that turned on the problematic features (Scrape Shield, etc.) anytime between last September and last weekend. Cloudflare should supply the full list to all the known search engines including the Internet Archive. Anything less than that is gross negligence.
If Cloudflare doesn't want to (or cannot) supply the full list of affected domains, an alternative would be to nuke the caches for all the domains that resolved to a Cloudflare IP [1] anytime between last September and last weekend. I'm pretty sure that Google and Bing can compile this information from their records. They might also be able to tell, even without Cloudflare's cooperation, which of those websites used the problematic features.