Oh honey - I really feel for you so much. Dont worry bubba will get better.
I'm sure you have this already sussed but have you ruled out silent ruflux, reflux, colic and all those other ailments?
Also, do you leave her to settle a little when she wakes? I dont mean letting her scream but all babies have a little whinge when they try and go to sleep.. sometimes Allegra would mumble and have a little cry on and off for about 20 minutes before settling a little.
I also dont think you should worry too much about bad habbits at such a young age. I think you need to sort out bubba having regular good sleeps and then deal with the sleep associations. Remember good day sleeps reflect on good night sleeps.
I agree that perhaps a hammock might help and there are some great music for babies CD's which help too to settle bubs.
Good luck and hope you have a settled night