In a case like this, you need to be really carefully how you respond to your cat.

Think of it in terms of clicker training:

Your cat does a behavior that you like, you click, and give her a treat. You repeat that and then start spacing out the treats so only *sometimes* she gets a treat. But your cat will keep doing it, because even the thought that *sometimes* she will get a treat, is a powerful motivator. And she can ring her own dinner bell by doing that behavior that you trained her to do.

So when your cat wakes up and makes some noise, and you run downstairs and appease her, even if you only sometimes do it, you are conditioning her to do that behavior consistently in order to sometimes get what she wants. In fact if you only sometimes come when she calls to you, it may very well result in "well I'm clearly just not yelling loud enough or persistently enough so I'll do it MORE". So you have to be careful and sort of think through how you want to handle it. If having your cat sleep outside your bedroom, and not wake you up at night, and wait until you get up in the morning is really important to you, you have to condition your cat to know that her making a noise will never ever ever result in her getting what she wants. And the only way for her to get it is to wait. At the same time though, it's important to be realistic about it, and try to pro-actively make sure that her needs are met as well as they could be. So food, litterbox, water, a very desirable place to sleep (like maybe a cat bed high up somewhere with a heating pad?) and so forth.

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The little monsters 3

Good suggestions and somewhat along the line I was thinking. My biggest issue is getting my partner to go along with anything that allows the cat to cry for more than a minute. She has this mournful meow that sounds so close to "Mama" that people swear we have taught her to talk. She is absolutely manipulating us but my wife just melts when she hears that - and it is only for her as if I show up she runs past me to get Mum. Little swine! She is of course so adorable and loving that it's very tough. The one thing I do not want to do is damage the very special bond that is still developing. We have had cats before but this is very different - wonderful - and infinitely more valuable than an occasional sleepless night. Reading about Bengals did give me some sense of the difference but experiencing it is quite another thing. I realize most people here already know this.

Maybe you could try to make a more appealing sleeping arrangement for her in your bedroom? With a nice warm cozy bed, food, water and a litterbox nearby? It might not work, but it might be worth a shot?

As Scout is still intact the local boys will never stop paying an interest and will always come around - possibly spraying up your walls/windows too - and this may be upsetting by your girl, especially as she ages and becomes more territorial.
Is there any reason she isnt spayed?

If you plan to spay her she will be a happier less-hormonal girl afterwards.

As for her Human training ... this appears to be going very well for her and she is becoming expert at wrapping you guys round her little paw ;).

Your wife needs to get clever and calculating about this and look at the ''crying'' behaviour as efforts to manipulate you guys rather than a sign of actual distress. If she wants to help Scout gain confidence and a healthy amount of independence she HAS to learn to turn off the buttons that Scout is pressing.

I dont think Scout needs you guys to interrupt you sleep to make her feel safe... thats just her angle right now (thats working)... if she was fearful she could remain with you both in your room and only go out to peep/poop or eat and return back to you to feel secure if thats the issue for her.
I think its not ... I think she is just bored and wants company as cats dont naturally sleep for as long as humans... 8hours is a bit too long for her to be alone with no attention from you maybe?... she can learn that actually its not too long... and the world doesnt end if mum and dad stay in bed.

To break the habit of waking you guys up .. ill echo advice already given here and agree that [IGNORE EVERYTHING] is the best policy.
Fake it basically.
When she hops onto your hip/chest and licks your face (lol, or w/e she does) Fake it - pretend to be undisturbed. DONT GET UP.
After you have maintained your full sleep period without getting up for her consistantly she will (eventually) stop trying to wake you guys.

You do know of course that she will be totally fine (and safe) in the home while you sleep and doesnt need your company to get through the night ... its time to teach her this too.

(lovely pic btw)

I feel fortunate that Raiden will sleep most of the night. He will wake me up once -- usually between 3 and 5 -- so I can put out some canned food for him, but he will settle back down and either go in his enclosure or come back to bed. We have a one-floor home, so Raiden may fall asleep in his bed or on some blankets in the living room and then I'll wake up and find him sleeping in our bed. It would probably be easier if you did indeed have a bed and food close by your bedroom and she may want to stay closer to you. Cats are very independent. They say to ignore a cat in the middle of the night. But, I usually need to get up and go to the bathroom anyway, so if I'm up, I'll take care of his needs.

If you aren't breeding your girl, then you definitely need to get her spayed. That could calm her down quite a bit. I'm glad she's a security cat. Hopefully, you've got the windows and doors to your home secure enough that people cannot break in. I'm a very light sleeper (hubby is not), so when Raiden wants something in the middle of the night, he just comes over to me and head-butts me and I wake up, although one night I must have been sound asleep has he had to let out this huge cry for me to wake up.

I know it's aggravating .... but I don't know that your cat is lonely and wanting company. If she knows she can sleep in your bed and has slept in your bed, then she's aware that she does not have to be alone. There are some cats who are quite nocturnal and sleep much of the day and are up and about during the night. Just like a child, you have to readjust things a little bit. Good luck.