My advice, and you are not going to like it, is to bite the bullet and reinstall everything to the new drive.
Like you said, if you Ghost the drive, you will get the same problems on the new disk and you are back to square one.
Even if you do find all the files that each application uses and transfer them across, you still have the problem of the Registry. Majority of programs will make some modification to the registry, and then you are getting into a major headache.
A program like Partition Magic, I don't know if it works over multiple disks. My understanding of P.M is that once it creates new partitions, it then goes throuh the registry and makes any changes to program entries to reflect the new changes made. For example if Office was installed on the C: drive and then a new Parttion is made and the C: drive becomes and E: drive, then P.M will make the adjustments so the O.S knows that Office is now on the E: drive.
Havin said that, I don't use P.M a lot and I could bemistaken.
It may be simpler to reinstall the programs and O.S. and it may also save you a lot of p*ss farting around.
Best of luck.