the extra files

[dnanian]

Theoretical interface speed -- 800Mbps -- is not something that you're likely to achieve in real world situations. We're copying hundreds of thousands of tiny files, and a few large ones, and we're updating lots of metadata, time information, folder structures, etc. It's just not something that's going to top out a streaming data rate (although it does saturate the I/O channel pretty well).

The other files were likely temporary files or VM swap files, if you used "Backup - all files" as your copy script. They won't be needed, and have no meaning across a reboot.

If you don't want the copy indexed, drag the volume into the Spotlight preference pane's Privacy tab. That'll prevent the indexing.

Regarding archived files, as indicated in the User's Guide, you shouldn't mix a backup with "data" -- your archives. When you try to update the drive with Smart Update, those archives -- which aren't present in the selected files on the source -- would be deleted.

Instead, partition the drive into a storage volume and a backup volume, and put any data in its own partition.

Make sense?