This feels like my life exactly, except substitute 8 month old daughter. I had the exact same issues. My little one always seemed to want to nurse right before sleep and then would fall asleep at the breast or with a bottle from Dad. She would be put into the crib asleep. Everyone told me I had to put her to bed awake, but how do you do that when she falls asleep eating right before bed? And, we probably didn't help the issue because initially when she was 1-2 months old, she really seemed fussy at night so we'd hold/rock her until she fell asleep. Fast forward to 6-7 months old, and she now won't go to sleep without being asleep in our arms and then wakes up 2-3 times a night sometimes to eat, sometimes to be rocked back to sleep.
I swore I would never do Ferber ("cry it out"), so I tried the Sousa graduated extinction method. Stand with your hand on her back, then hand on her foot, hand on the bed, stand next to the crib, stand 2 feet from the crib, etc until she settled and went to sleep but that didn't work at all. Finally after several exhausting nights, we committed to do Ferber. Everyone I talked to said it is 2-3 nights of torture and then you're fine. What a joke! 5 weeks in, we were still doing it. She'd usually fall asleep after nursing/bottle, go to her crib asleep and then when she woke up, we'd nurse her, if she didn't seem hungry but just wanted our attention, back to the crib she went. we did 5, 10, 15, 20 minute increments. It was torture on everyone! We had to sit in our room with the fan going to try to drown out the cries. She would be pulling herself up in the crib and then falling, sometimes hitting her head on the way. And, on we went for 5, 10, 15 minute increments. Finally, 4-5 weeks in, I said we have to try putting her down awake. So, we did. We'd feed her, get her close to sleep but not asleep and put her in the crib. Again, she would cry. And, now that we were weeks into it, we'd wait 15, then 20 minutes. (Ferber method says first night 5, 10, 15, etc. Second night 10, 15, 20, etc, to I think a max of starting at 20). Well, we couldn't deal with 20. So, we did 15 minutes and Dad and I paced and cried through the whole thing, watching her on the video monitor get up and cry and not settle. Then, after 15 minutes, we'd go in, lay her back down, pat her back, not pick her up, spend 1-2 minutes and leave for another 20. VERY DIFFICULT! I completely understand. But, once we started this method of starting her in the crib awake, it really did take only 3 nights. And, the first night it took 20-25 minutes total for her to fall asleep, then 15, then 10. I understand where you're coming from. It's horrible to listen to her cry. You feel responsible for all those nights of nursing to sleep. You're worried maybe she's hurt or in pain. I really think it's all just getting her used to falling asleep on her own. Forgot whatever you've done in the past (nursing to sleep, picking her up, etc.). Just start a new plan and go with it.
Now she goes in her crib for all naptimes and bedtime when she seems tired. Always goes in awake, NEVER cries, might crawl around for a bit, but always puts herself to sleep. And, for the first time in 8 months, she is sleeping through the night. I hear her get up sometimes and stir, but she is able to put herself back to sleep without rocking. She doesn't need the nursing, but just liked the comfort.
It was really hard and I think I was in the same boat as you by doing the "wrong" thing nursing her to sleep all those months, but this system really worked and it is so good for her and all of us.
If you can't do 5, 10, 15 minutes, try 3, 6, 9. Something, but you have to let her cry for a bit. I don't think she is hurt or has gas, she has just grown to need you to settle and needs to learn to settle on her own.
Final thought, my husband heard that sometimes air filters help because they both give a soothing white noise and help prevent congestion which might be waking her up. We have a Honeywell Portable True HEPA Air Purifier model 17000 bought at Home Depot that works great.
Good luck!!