This sounds very much like the dog I fostered and then adopted so please don't take what I write for granted. If I could do it all over again, I wish I could have known to take the advice I'm telling you. And I very much appreciate you recognizing these behaviors as fearful in nature, by the way.
This dog sounds VERY neurotic and in need of some expert help. I wouldn't even waste time hoping to get lucky with a trainer or self help advice on this one. I would try to find a CAAB (Certified Applied Animal Behaviorist), ACAAB (Associate Certified Applied Animal Behaviorist), or a Veterinary Behaviorist.
You may or may not get lucky with a Behavioral Consultant. I wasn't. Many seem to be against medication that isn't alternative (homeopathic, etc.) for some reason.
CAAB, ACAAB, or VB
are top tier and it's my opinion from this alarming behavior that this is who you should consult with. This sounds like some serious anxiety and fear going on. Extreme separation anxiety is serious stuff. The waking up in the middle of the night and barking at a corner could be neurological, or psychiatric, like PTSD or even just signify hyper alertness. If so, can you imagine what the constant state of over arousal and raised cortisol is doing to her body? They can advise you guys if medication or other veterinary intervention is needed. Medication, when needed and used correctly along WITH behavior modification, is NOT a bad thing. Both enable the other to work better.
CAAB/ACAAB Directory of Certified Applied Animal Behaviorists — Animal Behavior Society: Applied Animal Behavior
Veterinary Behaviorist Find a Board Certified Veterinary Behaviorist ACVB
It may be expensive but it will save money in the long run (especially from floor repair from the house soiling and vet bills from a bike run over) and your sanity.
Please do NOT settle for any other kind of "behaviorist" because there are people going around granting themselves this title without any education to back it up. A mailman who hasn't met a dog until yesterday can walk in off the street and hang a shingle and call himself a behaviorist with no behavior sciences degree to back it up. Many would tell you that you need to be a stronger pack leader or other such nonsense that will waste your time and money.
And I agree. Keep this dog home in her element, or as much in her element as possible. Her home is probably the safest place right now, as scary as even that is. Until a behaviorist advises you otherwise.
I would try to get on this soon. And not as a replacement for seeing a behaviorist, but in the meantime, Fearfuldogs.com is a good resource for, you guessed it, fearful dogs. I wouldn't do BAT with this dog (respectfully fjm). If at rest, she's a 7, putting her at a 10 near the bike and bringing her back to a 7 away from the bike won't enable her to calm down and learn anything from it. It sounds like she's way too stressed for such an aggressive protocol. I'm not a fan of BAT for when dogs are fear reactive anyways. BAT involves unnecessary flooding for a dog, especially if they're as neurotic as this dog, it doesn't sound like she can handle it.
Think about it, if you're slightly scared of spiders, getting near them is flooding you but you're not so freaked out that you can deal and learn from the experience and desensitize yourself to being near them. You can think because the instinctual fight or flight isn't in overdrive.
But if you're deathly afraid of them, and overall neurotic to boot, getting near them is just going to freak you out in a horrible way and you're not going to be able to have any rational thought save, GET AWAY FROM SPIDERS NOW. Rational thought and learning won't be able to function over fight or flight mode.