After struggling with this for quite some time, I figured out a workaround for the Quicken E*Trade MFA issues. Because MFA works intermittently, the following method makes it consisten:
1. Log in once using your full password and security ID, and store the password in Keychain.
2. If the download fails, do not press “Sign In” in the sync window — it will fail repeatedly.
3. Instead, select the E*Trade account you’re trying to download. Then go to Accounts → Update Selected Online Account.
4. Wait briefly. You should be prompted only for the MFA security ID. After entering it, the account should download successfully.
Good luck