Final postcript:

After the system recovery, all my custom folder locations (documents, music, etc...) were gone, but the files themselves were still safely on D:. The C: drive versions of these folders included all exe and iso files, folder shortcuts, and I think a few others. I just deleted these old versions since my current stuff was already on D:, then re-did my custom locations. That went without a hitch.

I decided it's best to leave Local and Local Low on the system drive, moving only Roaming to the D: drive. Even before moving Roaming I noticed that all my firefox settings were gone, so after pointing Roaming to D: I just did a simple restore of my entire Roaming folder backup I made yesterday before adding the second hard drive.

I only appear to have to re-do my Quick Launch bar, but that's to be expected whenever you move Roaming. Quick Launch is finicky that way. Other than that, everything works and all my settings are how I like them.

So all's well that ends well.