Where do you need specific tools for JA.. well exept for scripting?
You can simply use old version of GtkRadiant and change the settings to match JA then compile your maps with newer versions of q3map2 that support "-game ja" key.
Anyways as seen here: http://www.qeradiant.com
new version of Gtk is coming but it's not out yet...
For those light "beams" or "fills" (what ever
) you should make simple brush and use trasparent shader, they are usually near black.