First, run a repair on the entire database with phpMyAdmin, then Optimize it.
Once you do that, come back and let us know how large your database is.
It may be easier for you to do this manually via a Shell command:
mysqldump -uUSERNAME -pPASSWORD databasename > filename.sql
Change USERNAME and PASSWORD (but not the leading -u and -p) to your MySQL username and password. It IS case sensitive, so an "A" is not the same as an "a". Same with the database name.
If you still need help, and/or want me to handle this for ya, PM me the specifics.