Re: Hard Drive concerns
If we're talking about plain old ATA drives with ribbon cables then yes, the first drive that you boot from has to have its jumpers set as "Master" (or CS, cable select, but explicitly selecting the "master" mode is more foolproof.)
The second drive, if connected to the same ribbon cable and the second connector on it, has to be set in slave mode.
Most computers have more than one ATA port on the motherboard, and if the other drive is connected on another cable entirely then it should also be in master mode. However, I'm assuming you're going to use the same cable, and since the old drive used to be the only drive it is almost guaranteed to be in master mode if you haven't changed that.
If you have SATA drives, of course, then the drives have their own dedicated cables and connectors and will then of course not have any jumpers on them.
If you cannot see the second drive, go to Control Panel, Administrative Tools and select Computer Management. Click on Disk Management and it should list any drives the computer can see; Disk 0 being the boot drive, Disk 1 being the secondary and CD-ROM 0 being the first (possibly only) CD/DVD drive, etc.
If your second drive is visible in the list of drives, but doesn't have a drive letter assigned to it, then it won't be visible in the "My Computer" box, for instance. To assign a drive letter to it and make it visible, right-click on the drive in the list and choose "Change drive letter and paths" and assign it a letter.
If you don't see more than Disk 0 in the list of hard drives here, your old drive is most likely toast completely and you can kiss your files goodbye, or get the drive to a specialist company who can extract the data for you at probably quite substantial cost.
As for the unreadable files, I'm not sure which files were unreadable but if they were unreadable on the new hard drive you may have some more serious issues with the entire system. Hard to tell just based on your description.