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Icons or shortcuts to programs on the old drive will not work if the program was installed through the registry. Do not be surprised about this since your computer, using a new drive, now has an entirely new hard drive and is accounting for your programs in a new fashion. Further, to get into certain parts of the drive, you may need to take ownership of all or part of the drive.
To get your documents, you want to go to each individual profile folder and copy these to the new drive. The ability to run the programs on the drive itself no longer exists, unless the program can operate without registry entries. Very few programs are still written this way.