When Migration Assistant won't work, what should be done?

I had to zero a hard drive, fortunately all of my data was accessible, and I backed it up on another drive. Obviously did a fresh 10.4 install, and all of the updates so the computer is now up to date.
How can I migrate everything to my new system folder, libraries, etc. I already did the Apps manually. The problem is that I used Desinstaller and accidentally removed panther system components that were still relevant to 10.4.6 (strangely enough).
Now I'd like to get my prefs, app support, and everything else to my new drive so my Applications will function properly (and registered again). Migration Assistant will not work because, while it is on another drive, it only sees my actual system folder that I use as a backup OS on the other drive, not the folder with my old system files that I backed up myself there.
So any programs or applescripts to set this up, so that prefs go into their new spots in the proper folder hierarchy?

if u own or buy a usb hard drive on ur pc find ur itunes folder that hold all ur app music and pictures etc
copy it on to the drive then copy it to ur mac
then open itunes up and c if it has found u data if it has hook ur ipod up
if its not found it u need to copy  all data from the folder to the tab in itunes

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