Used Acronis Disk Director on my desktop, plugged in the laptop drive 240GB SSD (USB) and the new hard drive 500GB SSD (usb) and the copy seemed to be fine. I didnt see any error messages but I didnt stare at it for 3 hours either. The clone disk of course the Toshiba hidden restore partition, the primary partition C drive and the active (boot?) partition and yes, did check box for copy NT signature.

The computer boots up fine most of the time, but it seems that when the computer goes to sleep (i believe its sleep, hard to do much testing during school) or hibernate or reboot it will sometimes display this message:

Intel(R) Boot Agent GE v1.3.52
Copyright (C) 1997-2010, Intel Corporation

PXE-E61: Media test failure, check cable
PXE-M0F: Exiting Intel Boot Agent
Insert system disk in drive.
Press any key when ready...

Of course any key does nothing but repeat a similar method. However, if I press the power button on the laptop (Toshiba Portege R705, Win 7 Pro 64-bit) it puts computer into hibernate. After hibernating I press power button again and it comes out of hibernation without any odd messages or problems described above... so apparently that is my TEMP fix.

Another recent issue I noticed is on occasion when creating a new folder or modifying something in the system variables, other random areas I will get a message: "The Stub received bad data" and simply retry the task and it works. Perhaps these two issues are linked.