Sound's like you're in a very vulnerable position. You have one thing going for you, and you have one big problem.
What you have in your favor is that you know what you're feeling is paranoia (you used that word quite a bit about yourself). And you know you want to get rid of that feeling.
Here's the thing - paranoia doesn't just get wished away, you can't banish it, you can't reject it, you can't hope it will just vanish. You have to attack paranoia at the root cause - which requires deep conversations with those important people around you.
Now here's the problem - they're not going to be the ones to prompt this communication, because they're not the one's who feel like you do. Your room-mate seems fine cuddling with your new love, your new love seems fine saying he's mono but cuddling with your room-mate (obviously this makes him feel good, regardless of what he professes about his mono nature).
So what makes you feel good here? Everyone else seems to be satisfying their needs to one degree or the other.
You need to get a bit mad - at yourself - for letting this go on. You're poly, but that doesn't mean it's ok for your new love to cuddle with your room-mate. That's just how you feel, you don't have to come up with some logical belief to justify it, it is simply you.
Tell them this bother's you, because it sound's like it really does. Even though you indicated otherwise. And tell your new love to stop the cuddling, ask your room-mate not to do this behind your back. It's not on. And if they refuse, well then you have a choice to make, keep one or both knowing how they feel, or get rid of them out of your life. At least you'll make a stand about who you are and what you are comfortable with. This is a boundary-setting moment for you. What you do now will be something you'll look back in in years to come, so do the right thing, keep emotions to a minimum, and talk to them directly about what your limits are and how they make you feel.
That's my 2 cents.