hi andrea,
i had a bit of a problem with the swaddle too, he needed it for a sleep cue but wanted to get out of it, and could not sleep without it....ugh what a situation to be it.
i just keep one arm in the swaddle, then place him in the cot, hold the other arm down (mines a tummy sleeper) and rub his back to soothe him (he hates the patting).
viv has been an independent sleeper for a while so once he starts the mantra cry or the moaning, i just keep my hand on his back and stay there.
i did have a rough time for a bit teaching him to sleep un swaddled, hang in there she will learn very quickly.
(i tried completely eliminating the swaddle but it did not work for viv).
i would suggest trying to soothe her in her cot with your words/touch.
use pu/pd. pu to reassure and pu gently.
do not feed her (good on you for weaning her off the boob at nap times)
it will be hard for a week or so but the results will be so worth it.
let me find you the pu/pd link.