Lost mail on upgrade

I recently updated a friend's computer from Tiger to Leopard(10.4 to 10.5) and though I have tried what I think is everything, all of the emails are gone. I had previously upgraded her from to tiger(to 10.4) and at that time I remember that it was a real pain to import her emails and this time they just do not exist.
During the previous update I had to export her emails from os x mail.app 1 to entourage and then to the new mail.app 2 because for some reason it would not import correctly. After I did that, though, all seemed to be fine. Then she had some imported mailboxes which she kept for reference and then made a whole new set of folders in 10.4 mail.app 2.x and all seemed okay.
The upgrade was a little bit of a strange procedure because she has an imac flat panel with a g4 processor(unsupported for 10.5 installation). So I had to use Super Duper to clone to a GUID partitioned harddrive, upgrade and then clone back(I won't go into details but it took forever mostly because of the USB 1.1 only ports) Everything else works perfectly including time machine, which I had read might be a problem. The only thing wrong is that all of the mail is lost.
Now I have still an original clone of her old hard drive for backup so I have been taking runs at trying to fix it but am coming up empty.
Tried: in mail using the import function pointing it at the old hard drive's Username/Library/Mail folder. This comes up with mailboxes but no items in them
Tried: copying the entire username/library/mail folder over to the same spot as well as the appropriate .plist file with no luck, again it gets mailboxes with nothing in them.
Tried: emailchemy pointing it at the old mail folder, nothing
then I started reading more about the emlx files etc. and I looked at the username/library/mail folder for emlx files and the funny thing is that there aren't any. All there are are mbox files.
So I think from all I've read that 10.4 mail stored all messages in emlx format and those are supposed to be in the mbox in messages seen as a whole bunch of individual files but either these are gone magically or I can't see them. Or maybe because of the old import this has somehow messed things up.
any more suggestions?

Well, kind of. When Super Duper was running it repaired the disk permissions before copying over the information. So in that way disk permissions were repaired several times along the way.
I now have copied the username/library/mail folder over to a zip drive and am running filesalvage on it to see if it can see any emlx files lost in there.
One other strange thing of note is that the mail folder is 1.91 Gigs in size normally but if I compress it it becomes 16Mb in size. This kind of speaks to the fact that it is structure but missing the content???

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