Reapplying to PhD program after Master's
Your masters program experience will likely give you a boost if it will make your letters less generic and you can demonstrate research experience. It's possible some programs will not think you worthy, I don't know how self-absorbed those programs are in physics, but in biology a commitment and talent for research are prized above classroom performance.

I wouldn't stress so much your former poor application and instead focus on your recent successes, and use your personal statement/whatever equivalent is available to make clear your goals, and you could also use that space to reference your goals for your masters. Paraphrased, "In my masters program I set out to accomplish _______. Now I would like to continue/add to/expand towards ________."