I just did a properties on one of the gmail inboxes, and it was still huge. After I started to post this message, it had shrunk, so I think my configuration file will continue to shrink It takes a while. So my main problem is why do the gmail emails go to archive and do the messages get deleted from archives when I delete them from the inbox and then empty the trash.

Perhaps read this document which explains the oddities of gmail as an IMAP provider. I think it answers your questions. https://support.mozilla.org/en-US/kb/thunderbird-and-gmail#w_understanding-gmail-labels-and-thunderbird-folders