It sounds like you have large .pst files holding all of your mail. It is a tedious process cleaning up your mail, I recommend creating multiple new outlook data files labeled by year the were sent or received to archive your mail into these can be considered your two groupings. After creating these new data files you can start dragging over email and folders that are okay with archiving to the new data files. By doing so you will no longer run the risk of corrupting large .pst files that can take hours to repair.
Outlook really is the best tool for managing and organizing your folders and mail.