Wow, it sounds like you have your hands full too. Milo used to be the exact same way for the first 8-9 months of his life. Just incredibly submissive and would roll over for anyone and dogs and he'd pee himself if someone even looked at him. That passed, although he is still submissive with other dogs and he's pretty friendly all around except for the barking. He barks to get attention. If there's a new person or a dog around and they're not paying attention to him, he'll bark uncontrollably. I think this is my fault entirely though, for not teaching him that this is wrong when he was a puppy. I'm especially beginning to realize that now that I have been spending a lot of time with him and really trying to train him.
Thankfully he's never been aggressive, but he does like to play-bite. I'm trying really hard to get him out of that habit. When he puts his teeth on my skin, I make a loud noise to get his attention and tell him "play nice." If he stops, then I give him lots of praise, tell him he's a good boy and keep playing. If he continues, I stop playing with him and ignore him for a little while. This seems to be working. I think he's really beginning to understand and now stops most of the time when I say "play nice."
Milo is pee pad trained too and I had the same problems as you do. I had to block off my bedroom with a puppy gate because it has carpet and he kept going on it. He also kept going on the kitchen rug until I removed it. He was also peeing on the legs of the couch and the TV stand. My hard wood is pretty much wrecked because of him. So, I'll tell you what I did. The repellent did nothing for me. I ended up cleaning the wood and then spraying lots and lots of this vinegar, alcohol and lemon juice mixture I made on it and he hasn't gone in those areas since. Just make sure she can't smell the pee on the wood. When I saw him go on his pee pad, he got tons of praise and his favourite treats. If I saw him go anywhere else, I held him to show him what he did and scared him as much as I could and he'd run away. I also crated him at night and as soon as I let him out in the morning, I would take him to the pee pad and say "go pee pee" over and over again. If he left the pee pad, I'd put him back on it and repeat "go pee pee." After a while he eventually went and when he did he got tons of praise again (I'd tell him "good boy, pee pee," lol) and his favourite treats. After a while of repeating this over and over ever day, now I put him on the pad and say "go pee pee" and he goes right away. He hasn't had accidents in almost a month, which makes me just ecstatic! It also means that I don't have to crate or x-pen him when I'm out of the house. The last "accident" was when I stayed over at a friend's place and when I came back in the morning, he had gone on the kitchen tile, but I think that was out of spite for leaving him alone all night.
I tried something new with him today. I was playing with him on the couch this morning and I put him on the ground and said "go pee pee" so he ran to the laundry room where his pee pad is and went pee. That's my biggest accomplishment with him so far, but it took a long time. But I still don't let him into the bedroom where there's carpet and I haven't put the kitchen rug back down. When he was little, he didn't realize he could go to the bathroom outside, so I'd have to put napkins down on the ground to make him realize it was the bathroom. Now when I take him out, he goes pee, but won't go poo. He'll wait until he gets home and then does it on his pee pad. That doesn't really bother me though. As long as he's not doing it where he isn't supposed to, I'm good to go.
When Bailey screams in the crate at night, do you guys give her attention? Milo used to do that when he was a puppy and it was so loud! There was no way we could sleep like that. So I'd take his crate into the bathroom and close the door (so I couldn't hear him) and turn the lights off and go to bed. Eventually he realized that the screaming wouldn't get him attention and now he's quiet in his crate.
Milo still barks when he hears someone at the door. We live in a condo, so he hears people getting on and off the elevator or something. I can't even hear it, but he does and he starts barking. So, I spray him with water and that helps, but at first he'd run away when I sprayed him and then I'd chase him around trying to get him and he'd hide under furniture and not come out, etc... He thought it was a game. So I took the advice of ScootieBootie on here, who told me to "wear my dog" which meant attaching him to me at all times, so he couldn't run away from me. I used one of those flexi leads and put it on my belt:
Flexi Elegance Belt Leash - Collars, Leads & Tags - PetSmart
I don't use those outside because they don't give me a lot of control but for this purpose, it was perfect! After getting the squirt and realizing that he couldn't get away, he's starting to run away much less now and the barking at home has improved significantly. Outside is another story since he barks at everything that moves. I just bought some squirt guns to take them on walks with me now that the weather is nice and he'll dry quickly. But I haven't used them yet. Hopefully they'll work.
Milo also HATES the car! When he realizes he's going int he car, he stops walking and I can drag him all I want or bribe him with treats, he won't even see them. He just doesn't know what to do with himself. He's quiet but shakes constantly and looks like he's having a heart attack. When I take him in his hard crate, he throws up. If I take him without the crate, he freaks out and tries to jump all over the place. I just got him a Sherpa bag because we're going to be travelling soon and he does better in that one. But still the car is a challenge. I don't really know what to do about it either.
I used to have a great dane and just like your mastiff, he was the most well behaved dog ever. I think it's something about the terrier personality that makes them hard to train. They're like little dogs from hell. I should pick up Ceasar's Way. Thanks for mentioning that.
It sounds like she's got you pretty frustrated. I decided to return my shock collar before using it because it seemed a bit harsh when I tried it on my skin and the suggestions that were made on here started to work, but you know your dog best. You decide whatever you think is best for you and her. It doesn't matter if people tell you that you're mean or it's wrong. They're not the ones dealing with a crazy dog day and night.
It really does take a long time and a whole lot of patience to try and break their habits though. It's like trying to teach them that everything they have come to know as acceptable behaviour is now wrong. The "wearing the dog" thing really does help though. That way you can catch them right away whether they're doing something right or wrong and act accordingly. Don't give up hope, it'll work out in the end. I wish you the best of luck in whatever you decide. Let us know how it works out.