Robert:
You've sure got me confused.
For starters, more info about your system is needed. Exactly what drives do you have in it now? Was it just one drive for everything to begin with, or did you have separate drives for your OS/Programs and Data?
What do you mean by "I cloned the Drive contents"? Exactly how? What software did you use and do you mean you created a disk image backup of the drive, then restored it to a partition on another drive, or did you use software to clone the old drive to a new drive.
Be specific.
Look.... There are one of two ways you need to go with that kind of thing. Vista is very picky, and the new drive will need to have the exact same MBR (Master Boot Record) and Partition Table as the old drive. You can't just backup one partition and restore it and expect anything to work, as it's got to have the same boot loader layout, partitions it's looking for, etc.
One way to do that is to create a full disk image backup of the failing drive (storing it on an external drive). Then, restore that disk image backup to a new drive.
That way, you have a drive that looks exactly the same to Vista as the original drive, including the Master Boot Record, all partitions, etc. Then unplug the old drive and plug the new drive into the same SATA connection used by the old one. That way, you don't need to worry about having a different drive order and boot order in BIOS (as Operating System Boot loaders are usually going to distinguish between the first drive in the system, second drive in the system, etc., even if you change the boot order. Vista is very picky about that kind of thing.
The other way to do it is to clone directly from the old drive to a new drive, making an exact sector by sector copy so that the new drive looks the same to Vista as the original one did (same Master Boot Record, partition table, same partition sizes, etc.)
That accomplishes the same thing as restoring a disk image backup. Again, after you complete that process, you unplug the old drive and plug the new drive into the same connection so that you don't need to worry about drive numbering differences and boot order changes, so that the new drive works the same was as the old one and looks the same way to Vista as the old one did.
Only after you have a new drive in place that's an exact copy of the old one do you attempt to change any partition sizes (using Vista Disk Management for that purpose). Otherwise, I can virtually guarantee you that you'll need to use a Vista Boot DVD to repair the boot loader (since Vista usually balks when it sees any changes to partition sizes when a different tool does the resizing). That's not a huge deal if you have a Vista DVD handy. But, I'd avoid that problem entirely if I were you.
Hopefully, you haven't done any unrecoverable damage by doing something like trying to rename volume labels on the original drive and can't rename them back again. Never do that kind of thing when you have a failing drive until you get a full disk image backup of it (not just the partitions, you want the entire drive with the MBR, etc.).
My advise would be to try and get back to the same place you were before you started that process (with the original boot drive the only one working, setup exactly as it was to begin with using the same volume labels, etc.), so that it works with the new drive unplugged.
Then, plug in the new drive and boot into a Linux DVD like Mepis 11 with a tool named ddrescue installed on it, and clone the old drive to the new drive. Then, shutdown the PC, unplug the old drive and plug the new drive into the same SATA Connection it used so that drive numbering doesn't change. That way, you're booting into a different operating system to perform the clone and don't have to worry about issues like Vista trying to mount partitions on the new drive, etc.
When you do a clone that way, Vista sees exactly the same thing it saw with the original drive in it. Then, after booting into Vista, use it's Disk Management to make any partition changes desired so that you're using the free space on the larger new drive.
Let us know more about what you have and what you've done so far, and I can try to give you some instructions on using ddrescue from a live linux distro you boot into to do the clone for you.
ddrescue is specifically designed to copy failing media (that's it's entire purpose), and it can make use of a log file with info on sectors copied without errors. That lets it make multiple passes, only retrying areas that it couldn't copy OK during previous passes. When you have failing media, that lets you do things like let the drive cool off in between passes, since you usually start seeing more read errors when a failing drive heats up.
It's easier to use than it sounds (basically, you just download a .iso file for something like Mepis 11 (a free Linux distro), burn it to DVD and boot into it. then, use a few commands so that you understand how the drives show up and use a command to clone the drives (making an exact sector by sector copy of the original drive and writing it to the new drive, so that the new drive looks exactly the same way to Vista as the old one did (same Master Boot Loader, partition table, partitions, etc.)
A command like this would be used to get a list of drives in your system:
su
fdisk -l
Then, you could use a command like this to perform the clone (in this case, cloning from the first drive in a system labeled as /dev/sda to the second drive in the system labeled as /dev/sdb).
su
ddrescue /dev/sda /dev/sdb diskclone.log
Again, I'd give more info on your exact setup for starters (drives installed, etc.), and exactly what you meant by cloning the old drive (what software and technique you used), and we can probably give you better suggestions on how to proceed after getting a better understanding of your setup and what you've actually done so far.
--
JimC
Updates know where programs are installed too. I've operated this way for at least 5 years through 2 different computers.