Where is the motherboard speaker? That is where I would expect the noise to come from. You may want to open up the case and then power up while you listen. The beep codes usually do not point toward the hd.
You could use a program such as ghost to clone the drive or use windows transfer program to back the data on the external and then replace drive, install windows, do all your updates, install applications and updates and then do the transfer program to receive the files.