Is it possible to get into an elite physcis grad school for theory without having already taken graduate level courses? I'm about to embark on improving my PGRE score for the fall test (didn't do so hot the first time) and I'm wondering if it will even be worth the year-long effort. Also, I'm taking a couple years off to get research experience/pay off my student debts. 

I come from a small/medium school with no physics graduate program (wasn't interested in physics when I started, so I went with the place that gave me the most money), so I didn't have the chance to take any grad classes. I've also only had one semester of junior/senior level E&amp;M, QM, and mechanics (all that was offered). 

I've been reading different GRE forums and it always seems like the people who apply to (condensed matter) theory at elite schools like UChicago and get rejected still have a >90% PGRE and a number of graduate classes that they did well in. 

I got all A's in the classes I did have and there is a decent chance I'll have 3 publications (one or two as first author) from national labs, but frankly, after reading about others' failures, I think there is a serious possibility that all of this effort will be in vain.
Yes.  Graduate admissions committees at good universities are looking to recruit students who will publish a lot of high quality papers.  The best predictor of future publications is past publications.  By comparison, coursework is less important.  The Physics GRE is a very poor predictor of your ability to write good research papers.  

You should still pursue a good physics GRE score because it is a good measure of the student's ability to plan ahead.