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My guess will be some driver thats timing out.
if it is the pagefile try
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\Memory Management
ClearPageFileAtShutdown set to 0
Since the Hard Drive isn't blinking i doubt its pagefile related though.
Disable your network drivers and do a reboot cycle, twice.
Disable any services you can or drivers you don't need.
BootVis might show you something, but i don't recall that it times shutdown timeouts.
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