You're making this more difficult than it needs to be. Get an external USB/Firewire drive and use that to a data backup. do a file by file backup of your data. Download and run Spinrite 6 on your existing drive. Install your new ATA system hard drive as the slave drive on the same controller. Get Norton Ghost and make an image copy of your original drive to your new drive. After duplicating your system drive, take out your original system drive and change the jumpers on your new system drive to make it the master drive and reboot your machine. You'll end up with a new internal system drive, and an external drive with a backup of your data.
That’s more difficult, IMO. I don’t think there’s a problem with my system drive, but I could be wrong. I’d rather do this methodically, step by step, rather than throw money at it.
I can install the replacement drive as the Slave to the system drive on the same IDE cable, and copy from the current D: drive to the new one, without any other machinations.
If there are copy problems, then I can move to the next level of troubleshooting. I might still have a mobo problem, but that hasn’t been proven yet.