I installed dbus-switchboard which I hoped work as this is where .bittorrent files are handled, unfortunately since a magnet link is not a file but a type of URL I am not sure how to add it as a mime type.
So I installed browser-switchboard that doesn't help it just chooses default web browser.
It looked like if I could figure out a right click in about:config I could configure it but Holding the stylus in place just doesn't seem to work, this link explains the procedure, the browser works just like Firefox in this respect, so this IS the fix if you can get it to happen.
http://www.lamolabs.org/blog/7949/on...link-on-linux/
The issue is that I cant get the popup menu to fully show though it sticks in place when I pull other menus over it, white and unclickable.
in the end I edited /home/user/.mozilla/microb/prefs.js WITH THE BROWSER TURNED OFF.
after the line
<i>user_pref("network.protocol-handler.expose-all", true);</i>
I added
<i>user_pref("network.protocol-handler.expose.magnet", false);</i>
although it is smarter to add the <i>user_pref("network.protocol-handler.expose.magnet", false);</i> line in user.js in the same dir and then reboot the phone as I really scared myself by switching "network.protocol-handler.expose-all" to false and making it so I could not click on any links! Mozilla based browsers like Microb will add changes form user.js to prefs.js on restart of the browser(rebooting phone is best IMHO).
got some of this infro from http://wiki.maemo.org/MicroB_tweaks

At this point I still need to figure out how to get microb to see the magnet link as something to open with transmission but I will leave this for now as notes. Probably very simple for someone who knows how.