Try a Safe Boot (that's starting up with Shift key held down) which does some disk checks and clears certain caches. You should get to the OS X log-in screen eventually (it will take a bit longer than a standard restart), log-in to your normal account then shut down and start up as normal.
If no better, try downloading
OnyX and running all the options under its "Automation" tab, in particular the cache clearing options and resetting Spotlight (it could be stuck on the SpotLight process trying to index your new drive(s).
If it continues, check all hard drives in Disk Utility, and immediately on startup after a force shutdown - also launch Console first thing and check the "system.log" for any clues as to what's hung the shutdown process. My guess is some background process, maybe software drivers for a scanner/printer/USB device, etc. Check all drivers are up to date for USB/Firewire devices.