rescued cat may be sick?

This was a stray, I noticed it about a month ago, and knew it wasn't a feral by its behavior. It took over three weeks to win its trust enough to capture it which I did a few days ago. Since then I've become concerned.

She appears to be not quite full grown, slightly smaller than my cats. She may be pregnant, I'm going tomorrow to have her scanned for a chip and find out if she is.

She has been extremely lethargic. I kept her segregated for a couple of days, but now I pick her up and carry her out to the sofa. She immediately lays down and starts snoozing, and she has taken no interest in her surroundings at all. She barely raises her head to hiss at my cats when they come near.

She likes to be petted, but every so often hisses or growls for no apparent reason. Also hisses/growls when I pick her up no matter how gently I do it. I get the feeling she is in pain somehow.

Her appetite has been good, and she is using the litterbox.

She's a very nice little cat, and if no owner is found I will keep her. but I am concerned that something might be wrong with her. I've searched several cat health sites but I can't find anything that fits these symptoms. Any suggestions?

Boy I have no wisdom to offer, but that's so nice that you rescued her.  Smart to keep her segregated I would think.

thanks! She's a sweet little girl who definitely doesn't belong on the street. I was originally planning to take her to a rescue, as she is clearly part maine coon, but I got too attached during all those evenings of hand feeding her...

I now, they eat out of your hand and it's just impossible.  I think all the rescue people deserve medals because of their ability to keep taking them in and adopting them out. 

First of all, get her tested for FIV/FeLV and worms.  Don't allow her to interact with your kitties and don't allow them to use the same litter boxes.  After she gets the all clear from your vet, then you should be good to introduce her to your other cats.  Keep an eye out for any change in litter box habits, play habits, or eating habits.  If she becomes extremely lethargic, get her to the vet as she's probably coming down with something.