Scared of everything

I got both of my cats (Sophie 6 month old calico and Anna a 7 month old Tuxedo) from a Tuxedo and I brought them home two weeks apart a few months ago. Actually they were cage mates at the rescue and very close which is why I chose her.

Sophie fit in fine right away and quickly became best friends with my dog. Anna on the other hand has been skiddish since we brought her home. She was on the street for a while and then right into the rescue for a few months until I brought her home. I'm thinking something happend to her on the street because even though she loves us now, sophie and has grown to tollerate the dog, she is still skiddish over everything.

She is terrified of the vacuum and anything new she freaked out, runs and hisses, swats at the item. She is also scared of new people. Anyways, she has had bowel problems since we got her and we are trying to solve the problem. For the past few weeks she has been on meds and it has been very difficult since she doesn't like you doing anything to her. We have to give her liquid meds and shove a pill down her throat.

There is a rip in the fabric under the couch and she has recently discovered it and hides in there. I have blocked it now as there are nails/staples sticking out in there. I'm really at a loss as to what to do because since we started the meds she is now even scared of me and my boyfriend who she always follows, purrs at etc. Now when we approach she hides. I think it's a combination of all the vet visits/car rides/medications that are stressing her out but I'm am becoming concerned that she won't go back to her normal self. Even brushing, which she loves and seeks me out for it will still run from me when I try to brush her. Unfortunately if she has IBD then she will need a pill for life and this can't go on for the rest of her life.

Here's a pic of Sophie and Anna waiting for breakfast.