Lost all my preferences when I upgraded to Mountain Lion.

I upgraded my Xeon to Mountain Lion from Lion
I had my System and Apps on Drive 1.  I keep my data on Drive 2.
When I installed the new system the installer would not recognize Drive 1.  Said it was not "journaled".  It would not let me install the system without me wiping the drive.  So I Installed the system on Drive 2.
How do I get the System Disk (Drive 2) to see all my old preferences?
How do I get the new system to recognize all my Apps on drive 1?
How do I get all my Mailboxes, local mail and such over to Drive 2?  When I tried to import my mail the import wizard would not recognize Drive 1.
Thanks very much for the help.

I would
1. Boot from disk 1 to your old operating system
2. Get another external disk that us the same size in gb
3. Format the external disk as mac osx extended journaled using disk utility
4. Get SuperDuper  (free) and clone your disk 1 to the external
http://www.shirt-pocket.com/SuperDuper/SuperDuperDescription.html
5. Once disk 1 is cloned to your external check you can boot from external disk
6. Once booted from external disk then do an upgrade
7. After making sure all is ok on booted external then use SuperDuper to clone from external to disk 1
8. Boot to disk 1 after cloned and check again.

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