Additionally, I wanted to add a new "development". I did a registry compare (my taskbar has been different this whole ordeal) and I believe portions of user registry are missing. I did a reverse compare with RegistryChangesView (current registry -> backup hdd registry) which has a bunch of HKCU\Software\.. Keys and Values that are not present in the current registry (backup -> current seemed to show less differences, but I was having snapshot issues). When comparing with my tower that suffered a similar fate as this laptop, and with a fresh VM of Win7, I noticed that when all three are in safemode, the HKCU\Software\Microsoft\Windows\Explorer\ registry entry only contains SessionInfo\ for the two machines, with the VM having standard other keys. Taskband is the Key that works in conjunction with the Taskbar. The fact that the actual Taskbar folder where these shortcuts are kept (%AppData%\Microsoft\Internet Explorer\Quick Launch\User Pinned\TaskBar) has ALL of my shortcuts, but none are present on the taskbar, leads me to believe a registry problem is causing a host of other issues.
I have prepared two reg files, one to restore the "missing" keys and one for certain modified keys between the two. I do have another prospect, the RegBack folder has a reg copy (Windows but no ntuser.dat or usrclass.dat) the day I took the HDD out to copy files. Just before the trouble began.
I've made backups of the registry, but so we're on the right page, and for a second opinion, the locations are:
Windows/System32/config/
(I just took everything but it looks like 5 files mainly)
Windows/System32/RegBack/
Windows/System32/systemprofile/
(TxR and Journal left out)
Users/UsrProfile/ntuser.dat
%appdata%/local/microsoft/windows/usrclass.dat
I haven't tried booting normally yet or any reg changes.