To me, you seem like a strong candidate. I am unfamiliar with the Computational Neuroscience ranking of the schools you selected, but I'm certain they are all ranked in the top 20. As you mentioned, one weakness of your profile is your earlier grades. In order to counteract them, you must show you have improved by getting high marks in your current classes. This may also be worth mentioning in your statement of purpose.
I think GRE-Q scores at or above 160 are usually good enough for most PhD programs related to science, but since you are applying to top programs, this average might shift to 163 or 164. Since your score is GRE-Q score is 163, I think you are okay. Of course, your GRE-V score is high enough for any PhD program in science.
As for the rest, I think it is good. You have demonstrated that you have an interest in a specific area and are capable and willing to independently devote time and energy in the pursuit of knowledge related to that area. Since a large part of a PhD program revovles around independent research, your summer schools and projects will be a big benefit to your application.
As always, remember the admission committee considers all parts of your application, so a strong showing in one area will help cover weaknesses in another. Your letters of recommendation and independent learning experience will help make up for your first year grades. They should pose absolutely no problem if you can show you have improved with grades for the current term.
I apologize, but I can't recommend any other programs to you, since I am not familiar with computational neuroscience.
Also, if for some reason you aren't admitted to one of your choices, then you will have an excellent opportunity to make your next application completely ironclad. Because of this, don't slack off once your applications are sent, since you will want to be ready in case this opportunity arises. Think of how much you would then be able to accomplish between now and the next application season!