The first weeks were a blur to me, too. I still remember how hard it was for me, my baby is spirited when it comes to sleep.
She didn't want a pacifier either. We tried to offer her since she was 3 or 4 weeks and she always refused. Then suddenly, my husband had a luck, she took it from him. To be honest, it helped and it didn't. When she was sucking it she was OK but as soon as she lost it, especially if she was sleeping with a it she would wake up again for it and it was more often than without it. We just stopped using it within a short time.
Wait with a thumb, she will soon be more able to use it on more consistent basis. As for swaddle, my girl hated it but later, I found out that you should swaddle real tight, that resembles a womb environment, while lose swaddle is just good for nothing :wink:.
Regarding nursing. She is obviously nursing so long for comfort, as a spirited baby she won't go to sleep on her own. Anna was that way too, she would never fall asleep on her own, doesn't matter if she was rested or tired or overtired, she always wanted to be alert in case she would miss something. Of course, keeping her awake longer than she could take it backfired as she surely wasn't going to sleep if overtired, she would cry and cry. What worked for me was a sling. Not all babies like it from the very first moment but what you need to do is to put your baby in it and start to walk with her immediately. Your wife's movement will calm her down and she will feel secure because she will feel her body next to hers. It worked great for us, especially in evenings when nothing else soothed Anna. It is not very BabyWhisperer but in those early weeks you need to survive, right?
Also, within a few weeks, your baby will learn to suck more efficiently and she will eventually stay shorter on breast. Babies go from 40 minutes to even 5 minutes only at around 6-10 weeks. I know, for you it sounds like eternity but the time will just pass very fast.