I agree with everything DoubleClerk says, but I have a caveat to #3. As a 2L SA, I looked up the background of every litigation associate and partner I worked in my (satellite/manageably-sized) office. If they had clerked for a DCt judge (I didn't apply to COA judges the first time around), that judge went on my application list regardless of city/district. I made sure to do at least one assignment with each former clerk. At some point after I'd gotten positive feedback, I mentioned to them that I was (coincidentally

) applying to their judge, and I wondered if they'd mind talking to me about their experience clerking. They were all happy to do so, typically over a SA lunch or coffee. At some point during this informal conversation, I asked them if it was okay if I mentioned their name and the fact that we'd discussed the clerkship in my cover letter. Again, they all agreed - a couple volunteered to give their judges a heads up about my application. All of their names ended up in the first paragraphs of my respective cover letters - and almost every one of those judges gave me an interview. I mentioned that I'd done > 10 clerkship interviews, and this technique helped to get a few of those invitations. Obviously, not every ex-clerk or judge will be so receptive as the ones I was lucky to encounter, but this technique worked so well for me that I think it's worth mentioning.
This isn't to contradict DoubleClerk's advice that the 2L SA will not itself likely advantage or disadvantage you among judges - except that it will disadvantage you with the minority of judges who have a strong preference for public interest clerks. It's just to say that if you go to a firm with a strong litigation practice, the 2L SA is likely to offer you a rich source of former federal clerks. Use that to your advantage.