Here is my experience and some information for anyone who comes across a similar dilemma.
Well, I gave the WHS reinstall ~60 hours. Since I heard no activity from my drives, and couldn't get a picture on my screen, I finally became impatient and reset the machine. It rebooted just fine. After the reboot it came to the final setup prompts where it asked for my administrator password, then it logged me in to the server desktop.
At this point I was a bit frustrated, as none of the drives on the SIL3114 SATA ports were showing up (which I specifically loaded drivers for prior to installation, and verified they were recognized by the WHS installation before proceeding). I right clicked on My Computer and chose "Manage," and they simply weren't there. After checking device manager I realized I had quite a few piece of hardware which had no drivers. So, I installed drivers for the SIL3114, as well as some networking hardware which WHS didn't recognize by default. At this point all of my SIL3114 drives appeared under "manage" with the "DATA" label, but also with unique drive letters - which I knew was wrong.
Through all of this time my shared folders were recognized (ie, Music, Photos, Public, Software, etc) - however, I couldn't access them. If I tried to access them from the server desktop via the shared folders shortcut I received an access error. And by attempting to access any of them remotely, the folders simply didn't show up. I decided to update the server via Windows Update and see if that would help any.
After the Power Pack 2 installation and a reboot, all of my applicable storage drives were labeled as "DATA" and no longer had letters from the "manage" view. Also, my console view accurately displayed the appropriate size information for: total total size, free space, shared folders, and duplication (in reference to what I knew to be true before the reinstall). I thought I was in the clear.
Then, I began browsing all of my shared folders verifying that I could access them, and that all of my data was indeed there, and intact. It was all going well until I came to the final folder, "Videos." The used space for "Videos" in my console view was 1.08TB. Duplication was off, and status was Healthy. Yet when I right clicked and opened "Videos" I saw one empty folder and nothing else. So, I completely updated the machine (Power Pack 3, and all other available updates) and restarted a number of times. I retried accessing the Videos folder numerous times. Still, none of the data which was being reported as there, and which I knew should be there, was accessible.
So I came here to ask a question as to why this was happening, and attempted one more time to access Videos. To my great surprise all of the files and folders which were apparently just missing suddenly refreshed and were displayed. I have no idea how or why this happened. I'm glad it did. Perhaps it has something to do with the reindex operation - I have no idea. Anyway, I just wanted to share all of this information I had in case someone else finds it useful in the future.
