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The recommendations I would be getting would be from folks that still publish regularly (with academic faculty), or that are associated in some way with economics departments, although they may still be irrelevant, I'm not sure. That's my fear as well, though. I could always talk to different undergrad/grad faculty members about recommendations, I'm just concerned that one or two of the people I worked more with won't want to do all of that again.
Regarding the influence of the MS, I'm not entirely clear on how that influenced things. I did a combined BS/MS program, which means that some of my graduate courses are actually rolled up into my undergrad GPA. If you break them out, I think i wind up with a 3.78 undergrad and 3.82 grad, but I don't usually do that since it's a bit hard to explain. Actually, I feel like there are a lot of things that are a bit hard to explain about my profile, which I'm sure hurts a bit.
In terms of public policy PhD programs, I'm not planning on applying to those for a couple of reasons. First, I think that a lot of my interests (micro/game theory, and IO to some extent) are "pure" econ. topics rather than public policy topics. I also think that an Econ PhD is a bit more flexible, and doesn't necessarily "label" you (as I think the Public Policy MS has done for me, to some extent).
I'm not totally opposed to something like that, but I think an econ department would be a better fit, so I'd rather work a bit and improve my profile with an eye towards traditional econ programs (or related programs like MEDS, etc.)
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