I don't know if this is still relevant (and if it isn't, I'm sorry for necroposting), but I came across this topic in my search for a way to do exactly what the OP wanted, and I have now figured out my own solution, so I thought I'd share it.
As AJS said, the section of showthread.php pertaining to related threads starts at line 980.
Editing line 1000 from this:
WHERE t.fid='{$thread['fid']}' AND t.tid!='{$thread['tid']}' AND t.visible='1' AND t.closed NOT LIKE 'moved|%' AND MATCH (t.subject) AGAINST ('".$db->escape_string($thread['subject'])."') >= '{$mybb->settings['similarityrating']}'
to this:
WHERE t.tid!='{$thread['tid']}' AND t.visible='1' AND t.closed NOT LIKE 'moved|%' AND MATCH (t.subject) AGAINST ('".$db->escape_string($thread['subject'])."') >= '{$mybb->settings['similarityrating']}'
removes the criterion that the related threads must be located in the same sub-section of your board.
Thanks for this info, AJS. It was very helpful.
You may also want to edit line 1001 from this:
ORDER BY t.lastpost DESC
to this:
ORDER BY 'similarityrating'
so that the related threads are ordered by their similarity to the current thread rather than when they were last posted in.
Now add these two lines somewhere in the while statement, which starts at line 1009:
$similar_thread['forumlink'] = get_forum_link($similar_thread['fid']);
$similar_forum = get_forum($similar_thread['fid']);
Personally, I added them after line 1041 because we want to use the new variables in conjunction with the ones defined in lines 1039-1041 ($similar_thread['subject'] and $similar_thread['threadlink']).
Now, go to your showthread_similarthreads_bit template and edit line 3 from this:
<td class="{$trow}">{$similar_thread['threadprefix']}<a href="{$similar_thread['threadlink']}">{$similar_thread['subject']}</a></td>
to this:
<td class="{$trow}">{$similar_thread['threadprefix']}<a href="{$similar_thread['threadlink']}">{$similar_thread['subject']}</a> in <a href="{$similar_thread['forumlink']}">{$similar_forum['name']}</a></td>
and it should work.