"I let her know that although she has primary physical custody, she can not dictate the terms of our custody as that is something we have to jointly agree on, especially concerning the holidays."
On what basis was she given 'primary physical custody'? And why did you agree to this?
(You may need to keep the so so called 'relationship' to an absolute minimum and strictly legal and business like. No going to her for advice or to her aid. If she gets at your throat, end the conversation right there so you don't get dragged down into the muck. Remember she's feeding off you, both financially and emotionally, with a BF and there's child, this is no better than animal behavior and that should give you some courage.)