pees inside only all the time

I've been reading other posts and trying to do as much reading as I can about what I can do, but my 3 month old female puppy pees all the time inside. I have her in a crate when I'm at work for 4 hours and then somebody comes and walks her and then I'm back home in 4-5 hours. I put a small blanket in the crate for her and I swear it smells like urine when I get home, so I wish it often.

But what I can't figure out is that she will only poop outside, she will hold it and do everything possible to poop outside. She knows she's getting a treat when she poops outside, but when she pees outside she always seems shocked that I'm praising her and giving her a treat. I can't understand why she doesn't have this connection between peeing outside, but she has the connection about pooping outside.

Today it was pooring rain that I wouldn't have blamed her so much for peeing outside, but she scratched the sliding glass door and let me know she wanted outside bad. She went outside to poop and then came in and 5 minutes later peed in the floor.

I'm trying to clean the floors/carpet as much as possible, but I'm wondering if it's the smell of something left over? I've heard ammonia can cause a dog to want to pee when they smell it, so I'm trying to change to a vinegar/alcohol solution with my spray for cleaning.

I also haven't cleaned the cage in awhile, the metal part of it. I clean the blanket often, but not the crate. She sleeps in the crate and I've been feeding her in the crate. She was pooping in the crate, until I made her sleep in the crate and made the crate shorter and now she never poops in the crate. I see the mistakes I made and why she was pooping in the crate, but can't figure out why she will pee inside 90% of the time.