Hi, I had serious problems too! But i talked to Apple support and they are working on the mail fixes, as well as, some other serious issues. They took some information from my computer through various conversations with them and then they sent me the link to the Beta updates available to the public. This also allows me to continue to send Apple Feedback right away as it puts an app on your computer to send to them.
The update first one allowed me to finally open my mail program again without the "optimizing" issues where it was trying to upgrade my mailboxes which allowed me to starting using Mail again. I only had access to about 1%-5% of my old messages on my POP account but my IMAP accounts all worked fine. I also had the same issue you did, where i could only download my POP account email but it wont take my password to send so have to send from another account. i just got another Beta update yesterday and now I seem to have all my old POP email back in the folder but i still cannot send emails from the account as it won't recognized my outgoing password.
The only other critical issue I seem to be experiencing is the lost of disk space. when my mail started "optimizing" it seemed to drain everything bit of space i had on my computer so had to transfer lots of info to keep making room. BEWARE as when i loaded the Beta update, it still seemed to randomly take some of my disk space. guessing the mail program is somehow trying to make a copy of my folder like Photos does or used to do.... anyway, once I get all the missing disk space back and can send from my POP account, I believe things will be back to 100%.... I hope...
Here is the link to the public Beta updates. They stressed to make sure you back-up before using as it is for testing and feedback.
https://beta.apple.com/sp/betaprogram/
Hope this helps, Jeff