Help! Question on Backing Up/Installing New HD

[SargasoC]

Hi--
I've been experiencing wonky problems with my G5 for a while now. Disk Utility claims all is well; Disk Warrior can't even rebuild the directory, as it claims the drive is too corrupt. In February, I backed up the user files on the HD, erased the drive, reformatted it, and restored the user files for a temporary fix. Even today, Disk Utility sees no problem while Disk Warrior still cannot rebuild the corrupted directory. I just bought an new HD and plan on installing it today- but I'm really leery of backing up-- and then restoring-- user files if it's the directory files that are wonky.

My plan was to:
1. Back up the old HD (erase/zero-sum it for safety reasons, time allowing) on Firewire drive #1
2. Install the new drive
3. Boot up using Firewire drive #2 (with OS on it)
4. Install OS on new drive
5. Restart, using new HD as startup disk
6. Restore all files on new HD with backup program (I have iBackup as well as Super Duper, the latter of which I planned to use)

QUESTION: if it's a corrupt series of files in the directory, will backing up and then restoring all files (or all user files) merely replicate the errors on the new drive? If so, should I just pick and choose libraries (the Mail Library seems to be affected, for example) and files to manually restore?

I just want to end these problems once and for all.

Thanks,
Tasia