How to disable the number that the Email Registration module puts on peoples username on registration
I have figured out my own problem. The module has a double fail safe for there not being duplicate usernames. Every time a new account is created it adds the uid to the end of the username so that there would be no duplicates, but if there was still a duplicate it will append a 1 or 2 on the end. Since the odds of there being 2 identical usernames from emails I am just commenting out where it adds the uid and going with just the appending a number if it ever does happen. Here is the code I commented out:

/* 070715 AS commented this out so the user id is not concatenated to the end of the user name, 
this is just guaranteeing that no 2 people have the same username which has odds so small 
we aren't going to worry about it. 
  if (!empty($uid)) {
    // Put uid on the end of the name.
    $name = $name . '_' . $uid;
  }*/