> 1) There is no option to say "reply using the same 'from' address that the mail was sent to." ..

Used and loved this extension to solve that for some time: https://addons.mozilla.org/en-US/thunderbird/addon/594

> 2) ... the status icon/indicator will get permanently stuck in "new mail" mode and you have to restart the app to get it to disappear.

Rarely seen similar behavior in TB2 (no upgrade yet). Goes away when I hit 'get mail'. (Forcing it to check the server, and notice the mail is read. I do IMAP exclusively.)