Cat crying out

I've never owned a cat before so it might be simple, nothing obviously matched in the threads.

We got a rescue cat. She has been with us for about a month. She is around 4, and came from quite a bad home with 5 other cats all taken into care. She has never been outside. She had ear mites but I believe them to be gone now (given treatment have not seen scratching ears for a week)

She was originally very skittish and spent many days under the kitchen units or behind the fridge. I let her be for a week or so and then got her out and blocked them up. She was very nervous at first but now seems to actively enoy my company. Her spot is sitting on the kitchen units and if I go in the kitchen she jumps down for attention. She likes eating the treats out of my hands etc. Despite being very timid she does not scratch or bite unless being carried and trying to get out of your hands.

I have recently been letting her venture over the house rather than keeping her in the kitchen. However she doesn't seem to want to leave the kitchen much. She has also recently taken to crying out in loud long meows. I overfilled the food bowel and she has stuff left in there so she isn't hungry. I have put both water and milk out for her. She stops doing this if I go down to the kitchen. Most of the time it is just me in the house. I have tried bringing her upstairs with me in the bedroom, but if the door is open she will sharpish return to the kitchen. 

Is she just lonely and wanting company? Is there an better way to get her more comfortable upstairs? I was feeding her treats whilst I opened the door last and she bolted out as soon as the door was opened...

Any help/advice greatly appreciated. 

Cats only really meow for us. So I guess it sounds like your cat has trained you well, "Come forth human".
It sounds like she just wants attention. She'll explore and come out when she ready.
Try to give her ok places to hide. A box or under the bed. Cats like to have places to hide and somewhere high to "look around.

Deepest apologies if this comes across as pedantic, but just asking coz you said you were a new cat owner - by milk do you mean milk specifically for cats or standard store bought milk? 

Is she spayed?