How to make an MD more appealing for a PhD program in basic research (neuroscience)? 1 year and a half away from completing my integrated MS in Medicine, I have decided that, once complete, I won't be pursuing life as a clinician and want to do research in Neuroscience instead.

Now, I already have a paper published (jointly) and two more almost ready to be submitted, after having worked in both the genetics and pharmacology labs, where my tasks ranged from data gathering ("pen and paper research") to Western Blotting and micro surgery in mice.

My grades are not very good though, and I'm looking for ways of making my CV more appealing, besides asking for a summer intership in one the groups I like (all in Germany by the way).

Would having a specialization (Neurology, Psych, etc) be a plus? On which skills should I work?
PhD programs are wanting to recruit people who are capable of doing advanced research. Grades are a proxy that people use to try to estimate which members of a population (almost none of whom have publications) will be able to acquire the skill set necessary to publish in the future. And, grades aren't a terribly good proxy. Therefore, the best thing you can do to get into a good grad program is going to be to keep publishing, and ideally in the best places possible. 

If you publish research, then you'll be able to get letters of reference that talk about your skills as a writer and scientist that should offset any difficulty with your grades. 

You'll need to tell some kind of story to tell in your cover letter about why your grades are bad, and how they don't represent the work you will do in your phd program. (ideally a letter writer should address this fact too).

Good luck!