I'm going to suggest that you cross-post this to /r/legaladvice - because you really don't want to make any missteps while you're waiting for the live consultation with the attorney you're meeting with.
And I really can't stress just how important it is that you have an attorney involved in this process, given the accusations of abuse Jordan is lobbing your way.
I'm also going to second the advice you were given by /u/jpallan - especially emphasizing how important it is that you have Amy in certified day care or some sort of school program ASAP.
Even though you were in a poly relationship, and James is a legitimate part of your life even prior to the breakup with Jordan, you're going to be hard pressed to find a judge or child advocate who is understanding of, or respectful of, a poly bond. Prejudice about sexuality, gender issues and unconventional relationship models abounds... you sort of have them all brewing here in your situation. You do NOT want a judge looking at your case and deciding it's just one bit hot mess and ruling accordingly. You NEED more mainstream solutions and a more mainstream environment for your daughter during this process - or BOTH you and Jordan could find yourself fighting DCFS for custody of Amy.
That is the sad reality of our world, as disgusting as it is. Courts do not respect poly families... or the trans* population... and as an added bonus, they'll be scrambling to try and box you into a sexuality label they are comfortable with in light of James being male and Jordan being a trans* woman. Most of the people who will have power in your legal case are going to be very vanilla, and may just throw up their hands and toss the case to DCFS out of simple confusion and an inability to parse what is/is not "in the best interests of the child."
Now, for the personal/relationship side of things - no, I don't think you're being heartless. At this point, it is potentially dangerous for your daughter to be in the care of someone who accuses you of being abusive. I would not cut off access to Amy, but I would require that Jordan's visit be in my presence, were I in your situation. I'd also be inclined to keep a video record running during any interactions with Jordan, just for your own protection.
This really sounds to me as if Jordan is having a bad reaction to her hormonal treatments. It happens sometimes... I have a very good friend who absolutely went off the rails for about 6 months when she first started HT. She became paranoid, combative and extremely sensitive. She believed everyone was staring at her and judging her. She couldn't even go through a drive-through, because she'd claim that - while PLACING HER ORDER through the remote voice box well away from the window - the employee in the restaurant was talking about her with the other employees. People who could not even SEE her.
Once her body adjusted to the HT, she was mortified by her own past behavior. It was all so completely out of character, but she said that she felt as if she had absolutely no control over what came out of her mouth or her actions. She described it as being an observer in her own body for months, able to SEE how she was behaving and feeling ashamed, but completely unable to affect her own actions.
Jordan may be having a similar reaction to her HT. If you have the opportunity to speak with her doctor about any of this, that would perhaps be helpful - they may be able to ease back on some of the dosages to help her be a bit more in control of herself.