1. You should have gone through your recruiter definitely when trying to squeeze more out from the hiring company.
2. According to you, you asked for higher base, bonus and more vacation time. Instead, you probably should have asked for a senior position instead. Companies, especially large ones, have pretty strict compensation and benefits structure. You might have been asking for something that's out of the range of the same levels there, especially vacation time, which is almost a firm policy that nobody could change. Therefore, asking for a senior position would be a better choice, which will give you a better package for sure. If you had talked to your recruiter earlier, you might have avoided such a mistake.
3. You have been pretty lucky to still have some hope here; however, the chance is very slim. And you basically have no bargain power at all at this point. If the company is mean enough, they would offer you something less than the original one, and you might still have to accept it.
4. Talk to your recruiter now and stop calling that hiring manager everyday. Explain to the recruiter that it's not your intention to skip him to contact the hiring manager directly, and you did so simply because you didn't know the correct procedure here. Let the recruiter contact the hiring manager.
5. Other than that, nothing you can do but wait and start preparing for other interviews.