Check out a product called MailStore. They have a free version that makes indexing and searching through multiple PST files really easy. Can even pull down and index a copy of e.g. your gmail if you want it to as well.
I bet you'll find it useful.
Your question was posted in an IRC discussion on irc.mozilla.org in #thunderbird, BruceAJohnson answered (but couldn't publicly post in this thread):
> MailStore Home is a free program for home users that can archive and export e-mails from/to many e-mail programs. http://www.mailstore.com/en/mailstore-home-email-archiving.aspx
> @FireSomeonePlease For business use of MailStore, you pay for it: http://www.mailstore.com/en/mailstore-server.aspx
> From http://kb.mozillazine.org/Import_.pst_files Importing from Outlook and Eudora in the built-in import wizard was disabled in version 38 as they broke. You can work around this by using an older version of Thunderbird. So using MailStore Home is easier.
Actually one thing might be to archive everything in a separate archive--so if you delete something by mistake you will always have a copy. See for example Mailstore Home as a program to do this:
http://www.mailstore.com/en/mailstore-home-email-archiving.aspx
Likewise as mentioned set up separate folders for low priority stuff.