Did I NOT perform a Clean Install?

The answer I'd say is quite simple, using SL restore the document you want back.
Then create a partition on your external drive, copy those document/files to the drive, to your Lion clean install and then bring the files you copied back.

A clean install and then manually moving things back to your boot drive is not a good idea unless you really know what you're doing.

I would suggest you keep it very simple. Restore your drive to SL with all the stuff you had on there before using the restore function from Time Machine. Boot from your original disks and do a permission repair. Then install Lion by following Apple's directions; forget the clean install business.

You'll be much happier and it's MUCH safer than the hit or miss stuff you've been doing.

Rob

Zooby - if you are a MobileMe user and you have Sync Dock Items turned on, that's one explanation for why your dock has old items. Same with Dashboard items, bookmarks and other account settings.

Install lion.
Drag and drop your stuff that isn't in time machine into the proper places.
Plug in time machine
Open drive browse inside of backups.backupdb file to your user folder
drag and drop the music and documents files back to your user folder within lion.

Nothing hard about it hard really...