So, here is what I have done, and so far there have been no ill effects:
- Purchase Lion from the Mac App Store so that the installer is in the Applications folder before step 2...
- Download and register SuperDuper! and create clones of the boot and storage drives (since the Lion installer is on the boot drive, any restores will restore the Lion installer, preventing you from having to redownload it)
- Confirm that the boot drive clone boots properly, and that it still sees the original home folder (set up using the TUAW instructions mentioned in my original question).
- Run the Lion installer.
It was that simple. Lion installed over the Snow Leopard installation with no apparent issues.
The only "sort of" issue I have encountered (and it is not directly related to the OP) is that after installing Lion, I enabled FileVault. Since the boot drive is separate from the storage drive, and FV only works on the boot drive, I think this creates some sort of permissions issue when trying to access the storage drive, such that I was prompted for my password when performing many file actions (moves and deletes primarily). The biggest issue here is that anything that used Dropbox (on the storage drive) to sync, such as 1Password and TextExpander, was giving me permission errors and was not working properly. TextExpander lost the ability to use the Dropbox sync feature, and 1Password was throwing a strange sync error.
This did not happen prior to activating FV. Since the sensitive information is on the storage drive anyway, and nothing of any real value is on the boot drive, FV doesn't have a huge benefit to me, so I simply disabled it and everything seems to be working fine. I am currently investigating 3rd party encryption tools to replace FileVault.
I also had issues with Login items not staying put in the Pref Pane dialog (under Users & Groups), but disabling FV corrected that as well.