[Ham-Computers] Hard drive crash

[EUGENE]

Perhaps someone on the list can help me with this problem:
One of my PC's has a HDD (Maxtor) that was starting to fail. I installed a second HDD (Also Maxtor) and used their copy program to clone the original, but the pgm kept telling me that there were problems with the disk.
So, I did an XOOPY and copied everyting from the original disk to the new one. Then I re-installed WINME. (I know that when you clone a disk you can clone all of the problems, but these problems were with the disk and not the programs). Most of the desktop is as original, but over half of the shortcuts do not work and when I go to the actual folder, the program also does not work.
I KNOW that I should have backed everything up BEFORE this happened, but alas, I did not. (Since this happened, I bought a 250 GB WDD networkable backup system...)
So, the bottom line questions are:
 "Is there a way to 'transfer' programs from one HDD to another?"
(BTW, with the original HDD, it would work OK some of the time and about every second or third time of boot up, it would say Boot failure, insert a system disk.)
If there is anyone out there that can help me with this, it would be GREATLY APPRECIATED!
Thanks in advance,
Gene, WØQFC
Spring Hill, FL