Frankly, I never believed in the "early application, the better" idea. Programs meet at various times and often it may be as infrequent as once a month to review applications as a team. Therefore, in such cases (although admittedly every two weeks is probably more common) it doesn't make a hill of beans difference if your app was in the first of the month or the end, it gets evaluated in the same pile as everyone else. The early application "wisdom" comes from the belief that if you apply early, your application looks better because they haven't had as much to compare you with. However, programs have been evaluating candidates for years, so they know what looks good and what doesn't.
Now, that being said, you cannot submit applications after the November 1 deadline and it appears that even if you took Step 2 today, your scores may not be available before that date. This may very well hurt you at some programs if your Step 1 score is poor. If you are planning on sending in your Step 2 scores after the November 1 deadline, contact the programs to make sure they will accept it and evaluate it along with the rest of your app.
More competitive programs are more likely to want to see your Step 2 score, so it would behoove you to have your scores available to them. But again, you can't apply after November 1 (in some cases, October 15), and they may not accept your Step 2 scores after that date.
What's done is done - if you were worried about Step 1, Step 2 should have been taken this past summer. But can't change that now. Contact programs and ask if they will accept additional material (ie, Step 2 score) after the deadlines. If they won't, you'll have to decide if you still want to apply, whether or not your Step 1 is competitive.
