Kirsten,
Poor you AND Lily! But, to sound like a broken record...I agree with everyone else. Lily sounds like a nawteekat, bratty cat, kitten, not yet grown out of her ways. I truly do not believe it has anything to do with being outside for any part of her life. With the exception of Allie and Dakky, all my kitties were strays, spending much more time out of doors than Lily, and ALL have adapted to the inside life without any problem. (Well, not Minnie, but, she is a cat of a different stripe). I let my kitties out in the back yard, which is fenced, on occasion. I don't notice any more "I want outside, if not I will go crazy" behaviour from them regardless of when they have last been out. Please don't think you are being 'mean' to Lily by confining her. The sad facts tell us otherwise.

I bet she will grow out of it..though Allie, who is 4 this August, still acts like a crazy nut at times. I just smile, pick up whatever has been displaced, realize nothing in my house is that precious (besides them) and go on.

Good luck.