I have just been accepted into UW-Seattle's PhD program in economics, and I think many of my rejections had to do with had to do with my unorthodox background. Here are my two-cents, hopefully this isn't coming too late.
Of all the advice you got, the one that I thought was most useful was from rwillh11 who said "the biggest thing incoming poli sci PhDs are shocked at is the quantitative rigor of political science." and "Contemporary social sciences are all very quant heavy, if a bit less so than econ." I can confirm everything he says through the words of many of my professors. I just finished my master's in mathematical finance (financial engineering) which was a three-department program (finance, economics, mathematics), and also took some coursework with some of the finance PhD students.
Although isilya makes a great point that the committees care most if you can become an independent researcher, most committees will have a hard time seeing that potential if you can't handle the coursework ahead of you. Thus, his/her whole point that "Grad schools will care a little bit about the classes you take" should be taken with a grain of salt.
Think of it this way, top programs easily get more than 500-600 applications, probably closer to 800+ (think MIT, UCLA etc.). Many of these applicants probably have written some sort of low-level paper that has some econometrics in it and that's it. At the end of the day, most of those do not translate to a paper on the cutting edge of economics, so what is a good indicator for these programs?
The answer, if you haven't figured it out, is coursework. To me there are five primary things that most graduate schools use to evaluate you, each of varying importance at different times in the game.
1) GRE scores - terrible indicators of future success, the GRE simply offers graduate programs a super reduced-form initial assessment of students. If your GPA is not extremely strong but your GRE is out of this world (think V:165+ Q:170 AW: 5.0+), you'll warrant a second glance at least.
2) GPA - not a terrible indicator of whether or not you can handle graduate work. Like GRE scores, GPA works as a low-level indicator of your potential, although not all GPAs are created equal. The math major GPA is looked upon more highly than the history GPA though, so in this respect I think your focus is already in the right direction.
3) Coursework - although this will not indicate to a department how you are as a researcher, it is probably the heaviest factor that is given an initial glance. For example, take a student with a 3.5 GPA and a decent GRE of V162/Q167/AW3.5. If you were to