What you've written has more red flags that a May Day parade in China. This is seriously bad stuff.
I almost feel like she is having an emotional affair with him
She is going out of her way to talk/text with him for hours and hours -- far more time than she spends with you. That is an emotional affair (EA). She is stepping outside of the marriage and is giving what belongs to you to another man.
I know she isn't "Cheating"
Yes, she is. An emotional affair is absolutely cheating. The fact that you don't believe this is cheating is concerning and evidence that she has been working to gaslight you (i.e. to get you to doubt yourself).
she said he's her best friend and they talk about everything.
There is a long list of excuses/justifications -- just friends, it's harmless, he's like a brother (I suppose it is more likely to be "he's just my uncle"), he is a good listener, I don't think about him 'that way', etc. It is all designed to excuse the inexcusable.
I'm accused of not trusting her and being jealous.
This is flat out manipulation and control on her part. It's a standard for cheaters. It shifts the focus of the conversation and pushes guilt/blame onto you. And this isn't new, because you stated We are having marital issues stemming from my insecurity / past controlling behavior. Your marital issues aren't because of you -- you have a right to be insecure because she is a manipulative, lying, controlling cheater at heart.
Her mother told me that she's doing all sorts of things with him that she always tells me she doesn't like (watching horror films, going shooting, etc.) and stays up until 4 am hanging out with him on the couch.
The things she is doing with him underscore how deep of an EA she is in with him. In fact, what she is doing right now is "dating" him at her mother's house with her and your permission.
Being away from you and hanging out on the couch until 4AM? There is ample opportunity to take this to a PA (physical affair) and you should assume that this is occurring right now. Telling you that she won't communicate with you is just an additional indication of her intentions -- she wants to be alone with her half-uncle to date him and see if she wants to leave you.
How do I tell her I am not comfortable with the level of contact she has with him without sounding controlling and possessive?
Ditch the concerns about feeling controlling or possessive. Those are manipulative terms your wife uses to excuse the affair and get you to accept the affair that she is already having. You should be absolutely pissed because your wife has brought another man into your marriage. That is never acceptable and you shouldn't tolerate the lack of love and respect your wife is showing you.
My $0.02 is that you shouldn't waste any more time. Call your wife and tell her that you aren't going to tolerate her ongoing affair with her half-uncle. She can either come home right now or she can not come home at all. She makes a decision on the spot.
Prepare yourself for all kinds of excuses/manipulation ranging from you're just jealous/insecure/paranoid to she is just at your mom's for a family visit to she is confused/doesn't know/won't be controlled into making a decision. If she won't come home NOW and/or tries to buy more time/won't make a decision, she IS making the choice to be with her uncle instead of you and wants to continue the affair. Under no circumstances should she bring her half-uncle to your home regardless of what she decides.
From the sound of things, she is very manipulative/controlling/emotionally abusive, so you should prepare for her to refuse to make a decision. If that is how things go, you need to protect yourself and expose the affair.
1. Go see a lawyer ASAP and learn your rights. Find out what you can do to protect yourself. If your wife is adamant about continuing the relationship with her half-uncle, you will likely need to take steps to file for divorce to show her you won't allow her to continue walking all over you.
2. Tell those who you think could be helpful. Let them know that she has sidelined your marriage for her relationship with her half-uncle and has been pursuing him all day/night for months now.
3. Given your wife's childhood abuse, you may not really know how the dynamics of your in-laws works. Your mother-in-law (MIL) may know the extent of what is happening and even allowing her house to be used as a cover for what is going on. Don't be surprised if your in-laws end up aligning with whatever lies your wife tells, but that doesn't mean you shouldn't give them a chance to show they are honorable. Tell your MIL that you've had enough of her daughter's affair and that you've told her not to come home.