My ex-wife dropped my 13 year old daughter off at my door 3 weeks ago, she says " she is not allowed to stay over night at my house anymore". So what do I do? File for sole custody? Or wait to see if she will agree to the original custody order which was 50/50 joint legal physical. Because this is far from that.

I wouldn't wait around to see what happens next. I'd be in Court tomorrow morning filing for sole custody.

Your ex-wife cannot unilaterally (on her own, without your agreement) change the terms of the custody/visitation order. She doesn't get to "agree to the original custody order". If that's what it says, that's the way it is. Your ex, of she wants to change it (so that overnights are no longer allowed) is going to have to go to court and get it changed. In the mean time, if she doesn't obey it you would be able to ask the court to hold her in contempt.