var bar = $('.sr-list');
var subreddits = ['nba', 'madmen', 'gameofthrones', 'programming', 'python', 'starcraft', 'malefashionadvice', 
                  'wow', 'arduino', 'videos'];
bar.empty();
bar.append('<ul class="flat-list sr-bar hover">'+
           '<li><a href="http://www.reddit.com/r/all">all</a></li>'+
           '<li><span class="separator">-</span><a href="http://www.reddit.com/r/random/">random</a></li>'+
           '</ul>');
bar.append('<span class="separator"> | </span>');
bar.append('<ul class="flat-list sr-bar hover" id="myreddit"></ul>');
var myreddit = $('ul#myreddit');
var i, len;
for (i = 0, len = subreddits.length; i < len; ++i) {
  if (i != 0) {
    myreddit.append('<li><span class="separator">-</span>'+
                    '<a href="http://reddit.com/r/'+subreddits[i]+'/">'+subreddits[i]+'</a></li>');
  } else {
    myreddit.append('<li><a href="http://reddit.com/r/'+subreddits[i]+'/">'+subreddits[i]+'</a></li>');
  }
}

@@ -1,12 +1,13 @@
 var 
+$
 bar = $(
@@ -15,24 +15,77 @@
 .sr-list');%0A
+var $customBar = $('.flat-list.sr-bar.hover:eq(1)');%0A
 var subreddi
@@ -231,17 +231,36 @@
 deos'%5D;%0A
-b
+var i, len;%0A$customB
 ar.empty
@@ -267,329 +267,72 @@
 ();%0A
+$
 bar.
-append('%3Cul class=%22flat-list sr-bar hover%22%3E'+%0A           '%3Cli%3E%3Ca href=%22http://www.reddit.com/r/all%22%3Eall%3C/a%3E%3C/li%3E'+%0A           '%3Cli%3E%3Cspan class=%22separator%22%3E-%3C/span%3E%3Ca href=%22http://www.reddit.com/r/random/%22%3Erandom%3C/a%3E%3C/li%3E'+%0A           '%3C/ul%3E'
+children('span.separator:eq(1)').remove(
 );%0A
+$
 bar.
-append('%3Cspan class=%22separator%22%3E %7C %3C/span%3E');%0Abar.app
+childr
 en
-d
 ('
-%3Cul class=%22
+.
 flat
@@ -340,89 +340,38 @@
 list
- 
+.
 sr-bar
- 
+.
 hover
-%22 id=%22myreddit%22%3E%3C/ul%3E');%0Avar myreddit = $('ul#myreddit');%0Avar i, len
+:eq(2)').remove()
 ;%0Afo
@@ -437,32 +437,34 @@
 != 0) %7B%0A    
-myreddit
+$customBar
 .append('%3Cli
@@ -618,16 +618,18 @@
     
-myreddit
+$customBar
 .app

Use eq() to select correct elements