HTTP handler issues

Set the preference

user_pref("", "/usr/bin/firefox");

and point it at the launcher for Firefox on your distribution.

In addition, so Thunderbird can redirect some additional protocls (FTP and HTTPS) add the following
user_pref("", "/location/to/firefox"); user_pref("", "/location/to/firefox");
As well as that, you can define another FTP program to handle the FTP transactions (though Mozilla handles them just fine, try the following
user_pref("", "/location/to/ftpprogram");

Thunderbird extensions

Some extensions recommended by various users. Right click and save as to install these, because if you use MozillaFirefox it assumes it is an extension for itself.

DrewBroadley recommends:

OpenPGP message encryption and authentication. Requires platform-specific Enigmime extension
Forumzilla is an extension to Thunderbird and Mozilla Mail for reading news and blog feeds (all flavors of RSS plus Atom). It lets you read feeds using the familiar three-pane mail interface.
No New Window on Double Click
Prevents Thunderbird from opening a new window when you double click a folder.