As a Mum to a nearly 4yr old Cocker and nearly 9 month old human, I really think you need some proper professional guidance here.
This isn't as simple as preparing a dog for accepting a new baby (and you are right to have realised now that changes to Dora's routines should really have been made before the new arrival - it's not the end of the world, but it will make things that little more difficult) - Dora is a dog with issues, and you don't trust her - you need a professional to come in and observe her body language around the baby, to see if her grumbles are just adapting to the new situation or if she is stressed and anxious by the new arrival.
You are right, the baby will get scarier to Dora as he gets older - babies make strange movements which are unpredictable for dogs, and this can be difficult for them to cope with.
Honey and Isobel have been dong very well together - Honey is uncertain at times, and we've yet to face the crawling issue, but she has adapted well, but Honey has been encouraged to spend calm time up close with Isobel (and rewarded for doing so), and now that Isobel is reaching out she is encouraged to be "gentle" with Honey... they aren't in close contact unless we are right there with them, and once Isobel is mobile they won't even be in vague proximity without one of us there.... we have playpens, room dividers and baby gates set up to manage this... By completely keeping them apart you risk your baby becoming magnetised to the dog, and he will make much more of a beeline to Dora once he is mobile if he hasn't become accustomed to being around her - likewise Dora will be much more scared of him if she hasn't been able to suss him out in a safer (for her) situation.
If you do get a professional in, please please do make sure they are someone who uses positive methods and doesn't subscribe to the outdated dominance theories - these could cause problems for some dogs, but could easily be disasterous for Dora in her current situation - you need someone who can read her signals, and advise you on how to make her life less stressful... you need to be working with her rather than against her.
I must admit Honey was never banned from the bedroom - she doesn't spend a lot of time there, but for the first few days she liked to lie at the bottom of the bed while I rested in bed.... but she is very good at settling at the bottom of the bed, so I knew she wasn't going to come and trample over me when I was holding Isobel....
