Woah, and I thought the rescue shepherd mix I just adopted was super submissive. Nothing compared to that!
I don't have any advice for the puking, maybe get that checked with a vet if she's getting sick a lot.
To help with the peeing issues, try changing your tone of voice more than raising it. Coming from a shelter, there's a good chance that she's been mistreated in the past. If you're telling her off with a raised voice, this might take her back to a pattern of getting yelled at, probably followed by being hit, which she'd understandably be scared of and fear pees. It's about finding that balance of being authoritative with a firm tone rather than angry with a raised voice.
As far as her growling around you and the bed, I thought I'd pass on the tip a coworker who raises and trains dogs gave me - "don't allow her on the furniture for about a year". If you let them on the couch/bed/etc. then they may start seeing themselves as equal to you, which explains the growling at people and the other dogs around you. She thinks it's "her" bed and you're "hers". She needs to understand that YOU are the alpha, it's YOUR bed and you do not BELONG to her, rather, the other way around. Since that's seemingly becoming an issue she needs to lose furniture privileges, and see if that helps.
Remember, dogs are pack animals and they follow a hierarchy. The most important thing in a lot of issues is establishing yourself as consistently the number one alpha. What might help is if you can find another dog that is dominant over her, but will listen to you. For example, my roommate has a massive Rottweiler who's about three times the size of my little girl (I think she's got a lot of heeler or something mixed in, she's not even close to German Shepherd size) and is an extremely dominant dog. My little girl is very submissive to start with and rolls right over for her. However, the Rottie also listens to me, so giving her commands in front of my dog has really helped to eliminate the little bit of defiance that she had at the beginning. I'm dominant over the alpha dog - establishes me as ultimate alpha.