Reformat/Reinstall Question re Panther

Hi and sorry for any duplication of this questionin other posts.
I need to reformat a 160G HD in my Dual Boot G4. OSX 10.3.9
must be reinstalled. It is too late to use clone apps like SuperDuper because the drive was unfortunately already erased, and a manual drag-back of the entire contents of the
backed-up contents of the HD was performed, leaving missing
invisible files missing. Hence, System 9 Folder seems to be okay, but, for OSX apps there are certain apps - mainly browser/
email, which i would prefer to retain the original settings, and,
migrate existing email folder contents (inbox/sent box etc).
The browser is Netscape 7.2.
If possible i'd prefer to simply drag/drop over anything that i can
after wiping and reinstalling/updating the HD system back up to 10.3.9. I also assume that for my Sys. 9 folder (dual-bootable MDD) i can do a clean install and drag/drop prefs manually for the various apps within the OS 9 domain which i boot into independent and separately of OSX operation.
I'm looking for the shortest path by which to accomplish this
reinstall and to minimize the amount of individual application
reinstallations from scratch...wherever i can drag existing apps
and associated Prefs into the right places within OSX Panther.
Any advice much appreciated.
Thanks,
Mike

Cornelius, thanks and i will try to clarify as concisely
as possible;
Does this HDD have anything on it currently?<<
Yes, the HD does have elements of the previous OSX System
but will not boot from OSX (a result of the "drag-back" of
backed up content, along with my OS 9 Folder, rather than
being able to successfully use SuperDuper or other clone
app....
Do I understand that you backed up the HDD in question by copy by dragging to a backup drive, erased HDD and copied stuff back by dragging?<< </div>
Yes. As such, System 9 FOlder/Contents seems to be fine
having done it that way, but i recognize why OSX does not.
Are you planning to erase the drive again, install Panther, and repeat the process of copying by dragging?<<</div>
I want to erase/reformat the drive again, and reinstall Panther using proper Disk-Set procedure of restore/reinstall
but save original prefs of as much of the previous system(s)
apps (for both OS 9 and OS X) i want to save/preserve..
presumably having to do so by manual drag where possible.
Does this mean you want to repeat the process which you have already performed?<< </div>
No, just whatever can be salvaged for individual application
preferences, most importantly, Browser/Email (bookmarks,
inbox/address books, mail settings prefs)- within BOTH
systems... I would like to preserve, rather than having to
a) re-enter User Prefs, Mail Settings and also need to
keep existing Email in the respective browser mail apps.
Other apps, i can take the time to reinstall and re-enter
registration data.
I hesitate to make assumptions in terms of what you are doing. However, backing up and restoring by copying by dragging, while it works for simple data files, for some typs of apps, and for OS 9 System Folder and OS 9 Applications folder, will not give you the desired outcomes for other types of files. In OS X there are hidden files which are essential to the efficient functioning of the OS that cannot be copied by dragging.<<</div>
My questions above is to ascertain exactly what you have done so far and what the current situation is. We can then take it from there to see what can be done next to minimize the damage and enable you to recover in the best way possible.<<
I totally understand. the entire situation as it stands
happened due to some anomaly whereby using CarbonCopyCloner
(and SuperDuper before that) was sidetracked because both
programs reported inability to recopy "All Files" back to
the Drive (error message to that effect). To get back up and running in OS 9, I then just dragged OS 9 System back
onto the HD and have been using that environment only.
Soo, the bottom line is, i need to erase the HD and reinstall it all...but want to save whatever prefs i can
in the proper fashion. (Far more familiar with doing so in
OS 9 stuff than OSX)
Hope that addresses where i'm at with this and appreciate
your help.

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