When a few years ago there was a change to Rule 41 on warrants so the FBI could get a search warrant in a single district for cases where it was concerning computers in 3+ districts, the EFF flipped out, and the FBI said it was for malware removal?

Yeah, it was for malware removal:
https://www.justice.gov/usao-edny/pr/justice-department-announces-court-authorized-disruption-snake-malware-network

Justice Department Announces Court-Authorized Disruption of the Snake Malware Network Controlled by Russia's Federal Security Service

“Russia used sophisticated malware to steal sensitive information from our allies, laundering it through a network of infected computers in the United States in a cynical attempt to conceal their crimes.  Meeting the challenge of cyberespionage requires creativity and a willingness to use all lawful means to protect our nation and our allies,” stated United States Attorney Peace.  “The court-authorized remote search and remediation announced today demonstrates my Office and our partners’ commitment to using all of the tools at our disposal to protect the American people.”