I'm sharing this from a secondary account because I ended up sharing a good bit of personal anecdote here.
I would suggest that you take on a MS, but you also should consider changing your attitude towards your studies in general. For example, you state how someone could take every physics class at your university in two years, but on your profile you list yourself as staying for four years. It could be that you completed the coursework in two years and are staying at this institution for your research. But that would mean you dedicated at least a full year to your research, in which case you'd hopefully have multiple publications by now. So honestly, it seems like you are looking for ways to make things easy for yourself by taking as little physics coursework as possible.
You are repeatedly insisting that it is the school's fault you did poorly on the GRE. Do not attempt to deflect the responsibility of doing well somewhere other than yourself. I understand that your institution did not offer various courses and I sympathize to an extent with that. But don't act like you're powerless. There are many awesome resources like Kahn/Anderson, as well as the 5 PGRE practice tests you can find for free on the internet. In my case, my institution didn't offer a statistical mechanics course worth taking, and many of the other high physics courses were taught poorly (EM, QM, optics). But that didn't stop me from getting a 960 on the physics GRE because I took the resources available to me, and worked hard to fill in the gaps. You need to do something similar instead of whining about how your school didn't offer the courses (I'm sorry, that's what it kind of looks like, especially if you dedicated personal statement or interview space explaining this). You will struggle with a physics PhD if you continue to adopt this approach when things go wrong in research.
You write about how you are doing research on symmetry breaking, the Higgs, and dilaton fields. I won't pretend to know what any of those things are, and I've had substantially more physics coursework than you. How are you going to convince a university that you are at the cutting edge of high energy physics when you have only taken one course in EM and one course in QM? Personally, my research is challenging, but I have enough background to be ready to stand as an expert in the research. I'm not necessarily saying you aren't ready to challenge yourself with fascinating research topics (that's what research is all about), but the topics you have mentioned sound very 'pop-sci-esque' and the 'honors thesis' you refer to sounds more like an end-of-class report than a peer-reviewed research paper. I don't think you have yet encountered the drudgery that is typical of research done by graduate students.
You also reached way too high in the schools you applied to. Specifically you applied to Yale and other high tier schools. Students who get into Yale are extremely advanced in their coursework - many of them have taken literally twice the number of physics courses you have taken, many have taken graduate level courses before finishing their undergraduate degree, and most have GPA in excess of 3.5 from institutions with substantial grade deflation. Your physics curriculum which looks more like a physics minor than a BS degree isn't going to cut it at places like Yale or Dartmouth. I do not know if this is your ego getting in the way, or if your professors are encouraging you to apply to schools beyond your reach, but you should re-evaluate your list of schools and make sure you aren't wasting money and time on what I like to call 'ego-applications'. I was admitted into a physics program on a similar level as the Ivies, but I thought long and hard about even applying to the school because I was concerned that it was beyond my reach, even with how hard I've worked as an undergraduate.
There are many students like you who complete an undergraduate at a liberal arts institution with limited coursework, and then expect to immediately 'take the next step' to a physics PhD somewhere like Yale or Harvard without a clear grasp on why they are seeking the PhD. Why are you seeking the PhD at this juncture in your life? It seems to me like you expect to just 'coast' through a PhD instead of taking this opportunity to actually decide what you want from life.
Do the MS at a highly regarded physics institution instead of looking for an easy way out. Emphasize taking as much coursework as possible, because (especially if you want to go somewhere like Yale for a PhD) you need this opportunity to get caught up to the other applicants. Work closely with an advisor to do research which comes as close as possible to PhD thesis writing. If at that point you are still enthusiastic about physics you will then apply to be considered for a PhD.
Edit: I wrote these words out so that they might help someone. This isn't about money or undergraduate school prestige. Case and point, OP likely is from a FAR more affluent background than I am. I attended an in-state public institution with mid-rated physics, which was the best available to me given the circumstances, whereas OP chose to attend a private school which offered limited physics. The point is to just stop making excuses and get to work.
Edit2: For reference, the above poster left an edit where he/she insinuated that I come from a rich background with rich mom and dad doing everything for me, whereas the exact opposite is true. He/she edited it out before I could make my first edit.
Edit3: The above poster has absolutely no clue whatsoever about this situation. OP went to a private liberal arts university, which are known for having incredibly high tuition cost and selectivity, so money and lack of choice is clearly not the OP's concern. However, if your family makes pennies a day and your only realistic option is to go to an in-state school where the tuition is only 8K a year, it becomes quite clear who is the 'privileged' one. Also, it's extremely presumptuous and downright backwards to state that someone who understands the idea of work ethic and personal responsibility is 'privileged', which is a word being thrown around a lot to silence unwanted ideas. You can feel free to continue believing your delusion, but I choose not to allow myself to become a victim of circumstance and I choose to do what gets results in the real world while encouraging others to do the same, because it works.
Edit4: Thanks for entertainment
Please just let the 'privilege' thing go. I also come from a pretty shitty place and I have zero sources of privilege in my life (no 'rich mommy and daddy', zero parental contribution, worked two jobs to pay for tuition) but you are continuing to insist otherwise and make everything about privilege. Can you not fathom the ridiculous idea of someone earning their way to the top? Why do you seem to want OP to think there's nothing they can do to improve their situation?
Edit5: I'm not really sure why I'm editing this post again, since the above poster is clearly trolling at this point. But he/she isn't even arguing anything. I just want to say that it's becoming clear that this isn't about any kind of 'privilege'. This is about trying to silence a viewpoint you don't like. I could say I'm a black LGBT male (which is true) and I would still be 'privileged' to you. Evidently, privilege has nothing to do with being rich or from certain backgrounds, but rather anyone whose viewpoints you dislike is privileged. If you can't argue cogently with someone, just edit out your previous comments and call them 'privileged', right?