I was sexually assaulted by a professor writing me a LOR for grad-school applications. What should I do?
That's really awful, and I'm so sorry someone whose job it is to help you instead put you in this difficult position.  

When you applied for your masters program did you have strong letters from professors at your undergraduate school?  While all things being equal it is better to get letters from people who have interacted with you more recently, having one letter that's only a year or two old should be fine.  Since those professors already wrote you a letter, there's a good chance that they'd be able to update it and resend it easily.  This may be more practical than getting a totally new person on such short notice.  It also seems clearly better than only having two letters.