I don't think a 3.5 is the end of the world. I had something a bit higher, but I went to a pretty/very weak undergraduate school. They will care more about how you do in math classes (well, mostly real analysis) and to a lesser extent your econ classes. Good letters also help. A very good quantitative (they won't care about the verbal and won't care much about the analytical) GRE score is essential. The test is complete BS, but if you don't score an 800 it raises a lot of questions. Anything below 760/770 really hurts your chances a lot.

Those courses sound about right to me. The masters level micro/macro probably sends a good signal, though they may not really help you after you get to grad school (this depends on the quality of your institution. I took these kind of courses at my undergrad institution and they have no bearing on what I do now. But if you go to a better school they might be helpful. They probably send a good signal either way.) The other courses seem good. Work in as much math as possible and get good grades in your math classes, especially real analysis. I've heard that some admissions people go so far as to say that the only thing they look at is the grade in real analysis (this can't be the norm since there are many people in my program who didn't even take real analysis and this is considered a top school, but it at least makes some point).

Also, whenever you do apply, apply to ALL of the top schools, unless there are one or two you know you wouldn't attend (for me this would have been Chicago, I don't really appreciate the ultra competitive environment). It is somewhat of a crapshoot where you get into. I got into a school which is supposedly in the top 5 in the current rankings with full funding, but was not offered funding at a school ranked around 10, and rejected from a school not ranked in the top 15. So, IMO, your best bet is apply to the entire top 10 and maybe 5-10 other schools that you like. This is costly in terms of money since most apps cost around $50 or more, but if you're going to be spending 4 or 5 years someplace it makes sense to invest upfront in finding a good match. And in terms of effort, once you're up to around 5 schools or so the applications don't really take much additional effort since you can start recycling your statements of purpose with not very many changes. Best of luck to you.