I scored below 550 in both Level 1 and Level 2. I ended up with 30 interviews. At a really amazing community IM place with a huge amount of fellowships the PD told me during my interview that since the SD is almost 100 points for comlex that it doesn't really matter whether you scored 500 or 600.
You will have no problem matching into a reputable community IM program with fellowships. You will still have a shot into academic IM. Some academic programs you can apply to both primary care and categorical track and they consider them both the same (and you can switch tracks after acceptance, for example, primary care into categorical or vice versa). Not many applicants know about this and do not apply primary care thinking that they'll be stuck with it. This will definitely increase your chances. Unfortunately I only figured this out towards the end of my interview season otherwise I would have probably snagged a couple more Academic IM interviews by applying to primary care tracks.
I would recommend trying to get good LOR's, bust your ass for Level 2, and if you want academic IM, do research. You do not need research for decent community IM Programs.