Just in case someone else has the same problem I'm going to post my fix for this.
Seeing as how I didn't use the Local folders for any of the new mail and kept all the mail in it own "account" on both PCs (but the only thing that matters here is the new PC portion.) all I did was copy the mail folders in to the local mail folder. Oh yeah and the mail boxes are found in (in windows anyway)
C:\Documents and Settings\User\Application Data\Thunderbird\Profiles\zfgsoel6.default\Mail\
Seeing as how I wanted to use the Local Folders portion of Thunderbird go in to the Local Folders folder and paste the old mail file in here. Restart Thunderbird and do what you will with all of that mail.
Let me know if anything is unclear I'm trying to get ready to go to bed so things may not make sense.