What can I do to apply a math PhD based on my problems? [on hold]

I have some confusions on my application. May anyone help to answer my questions? It might be a little long. here is the information. I am now graduating from a master program in a top 20 math rank university and planing to apply a math PhD program.

1.I know it is very important for one to get good GPAs, but my GPA is very poor, which just satisfy their requirement. I am in a very poor school of math in my undergraduate, so when I was in the master program , I feel very struggle. I do not get good GPA in first year, and in the second year, I have some health problem. In fact, graduate courses in my school is hard to gain good GPA, professors do not give good scores. Should I say something in my PS? I don't know whether they will care. My friends says I'd better not since the school just care the result, no one cares who you are and why you are that.

2.I believe I have a good recommendation letter. I am doing a solution set to a graduate book written by my professor. He praisse my work and write a recommendation letter for me. I believe it is a strong letter. The other two may not be so strong, is it important to get three strong letters?

My GRE general is just OK, I know from my professor that, GRE general is not quite important. My GRE sub is 90%. I don't know it is high or not. since I can not try in this years, I may use this. Can my GRE sub somehow make up my GPA?

In fact, I am good enough in math. My GPA is poor since I can not adapt the academic life at that time. Now I have done a lot and I believe I am almost as well as the PhDs in my school. I don't know how to show that to the committee. You see, they looks at GPAs, but as the reasons in 1, I can not persuade them. Is there anything else to show? Like to require an interview. I am confident enough that they will find my math is beyond their admitted requirement if they have talked with me.

I want to apply a school of math rank around 20 to 30. Is it possible?Do I have advantage if I apply applied math? Someone says applied math is easier to enroll but my courses are all covered with pure math with advanced ones, like functional analysis, differential topology, and I sit in some courses like algebraic topology , complex dynamics or commute algebra.

Can anyone give a suggestion to which range of school I should apply? The most important is how can I show my math in some way to the committee.