I'd like to help, here, but you're not being very clear about what you've done, how you did it and where you want to go. How did you move these files? Did you just copy folders, try to drag and drop,have all hidden files shown? First off, you mentioned cloning the drive. If you actually did a successful clone to the new drive, you're done. The old drive's contents and OS are now put on the new drive exactly as they were on the old. Turn off the PC and set the new drive as the master, both by the jumper on the new drive and put it on the end of the drive ribbon, not the middle connector. Boot it up and enter your bios. Check to see that the drive is correctly listed. If it is and it ought to be unless you failed in the clone, reboot and you'll see your old box back. The new drive will be configured as drive C (normally) or whatever you opted for. I don't understand why you now want to format the old drive if it's shot, unless you want to see how long you can keep it alive and just use it for non essential data. I wouldn't be trusting it with anything vital. If it's a S.M.A.R.T. enabled drive, and it warned you it was failing, well...it's done or about to be so.

I don't know how you determined that your drive was failing but if problems were showing up in your filesystem, a fresh operating system install might be a good idea. It's hard to say if any system files were corrupted. You seem to have some trepidation about taking the old hard drive out. It won't cause problems as long as the jumper on the new drive is set to master (I'm guessing that it's your primary drive), plugged in to the end plug on the ribbon cable, and has an operating system installed on it. If you have all of that, you're ready to rip the old sucker out! I wouldn't recommend using it for anything else because you never know when it will fail on you for good. If the new drive doesn't have an operating system installed, don't fret! Cloning would be the easiest way to go but you can still do it the old fashioned way. Before you start, make sure you have: 1. The new hard drive. 2. Your operating system CD or recovery CD from the computer manufacturer. 3. Your driver CDs (they may all be on one CD from the manufacturer or on individual CDs for each device) 4. Your program CDs Remove the old hard drive and install the new one. Restart the computer with the operating system or recovery CD in the CD-ROM. If your computer isn't set to boot off the CD drive, you will have to go into the BIOS and change that setting. The install program should detect that the new drive isn't formatted and walk you through it. Follow the prompts for installing the operating system. Install the drivers for all the devices. If the driver isn't installed for something, it may not work very well or it may not work at all. Install a firewall and virus checker. Update your virus definitions!! Install your programs, restore your data, and you're good to go.

At this point, I would not take the chance that a trojan or other malware spreading to the new hard drive. Or a malfunctioning file could cause more damage. I would wipe it clean and put in a new operationg system and make it a slave to the new hard drive.