I think your high GRE score would get noticed. Of course it's very unlikely that it would be the reason that they would choose you, but I think that it would be noticed and may play some part in funding decisions. Your SoP and your letters would be much more important however, and if you clearly outlined your research experience and interests as well as how you would fit with the schools that you applied to, then that would help your application a lot more than your high GRE. I'm not sure how much the schools you applied to will consider the flags on your transcripts, but they do tend to pay a lot of attention to the last 2 years and they do like to see that your GPA has improved over the years. It's hard waiting, but I hope you get some good news soon. All the best!