Charles,
You didn't mention which version of QRecall you are using. If it's 1.2, then restoring a bootable Yosemite volume is dicey. Starting around OS X 10.10.3, Apple started adding a lot of new security requirements that a volume restored with QRecall 1.2 might not satisfy, and it's completely incapable of restoring an El Capitan system.
You did the right thing restoring the volume—boot from an external volume and restore your boot volume. Just make sure that your external volume has the same major version of OS X that you're restoring. It's often the case that an older version of OS X (10.9) will be incapable of restoring a newer version of OS X (10.10), because of new features Apple has added to the filesystem.
OK, so you've restored your boot volume and it doesn't boot. Don't worry. Starting with OS X 10.9, the best remedy is an over-install. After recalling your boot volume, boot into your OS X recovery partition and simply reinstall OS X over what you recalled. OS X is now very good about surgically reinstalling the OS. It won't overwrite any of your accounts, documents, applications, or preferences. When the install is finished, you'll have the latest OS and everything else should be intact.
Now, about capturing Mail. The Mail app uses a database. This is really difficult (read "impossible") to cleanly capture while you have Mail open. The best time to capture your mail is when the Mail app is closed.
If getting a clean capture of your mail is really important, and you're using QRecall 2.0, consider scheduling a capture of your mail folder and preferences "when Mail closes", using the new application-based event schedule. You can also have QRecall skip your hourly capture if the Mail app is open, or just hold until the Mail app closes. But if you're like me and leave your mail app open all day, that won't be of much help.
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