Stray Cat Behavor

:( I have this stray cat the we took in last sept. we got her shots and she was already spayed. she IS NOT a loveable cat at all but, has come a long way and will play with me as long as I don't pick her up. anyway she is avting really really strange lately. she uses the litter box (no problem) but, when I let her out she acts really weird like she is scared to death of something and goes in and out all day long. I have tryed EVERYTHING I know to please her. she does not eat alot like she use to. but, meows, jumps in the windows and continue to do this as if she is trying to tell me something. I don't know alot about cats as I was never a cat owner. she used to play with me several times a day as long as there is no contact of putting your hands on her. rubbing her head is ok now but didn't used to be. she is keeping me up at night meowing. I keep food and water in her dish so I know she's not hungry or thirsty. and, she is acting very strange when going out like is is scared of something and the same when she comes back indoors. sorry this is so longggggggggg but I need some advice as to what to try next. thanks for any infro you may have.