Hey, a few things from this post I can comment on. Sweet!
Right there with you. Our 9 month old got really congested in the last few days complete with cough, runny nose, and difficulty breathing through her nose. We elevated one end of her crib a bit with a towel underneath to try and help out, which only somewhat works. She sleeps a few hours in her crib, but the last few nights we've had to bring her into our bed and prop her up on a Boppy pillow to help her breathe, which has helped. Wife is home with her today, but she is actually doing a bit better, and her fever broke. Neighbor across the street has a newborn and a 3 year old, also both sick. 'Tis the season I suppose, fortunately it doesn't seem to last long, but does come back every month or so.
We had this exact problem as well. Did pretty well getting her to sleep in her crib around 6:30 - 7:30, would sleep for several hours, but wake up around 1 - 2 and wouldn't go back down in the crib. After enough sleep deprivation, we resorted to co-sleeping for a bit after that 2am night waking so we could all sleep (after trying a bottle, rocking her for an hour or so, all that - she would pop back up immediately after we put her back down).
We didn't want to do the cry out method outright, but opted for a more "gentle" approach, which centers on minimal interaction during those night wakings. When she awakes and cries, we do give her a couple minutes to see if she is able to put herself back to sleep, but if the cry is urgent or intensifies ("I need help!"), we intervene, while "interacting" as little as possible. If she has a wet diaper, we change it, if she's hungry, we feed her. We don't communicate with her directly (or each other actually, keeping it as quiet as possible), and immediately put her back down in the crib as soon as we've addressed the concern. If she cries, I put my hand on her back or rub her head slightly until she calms. Took a few minutes the first night. The next night we did the same, but after putting her down, instead of placing my hand on her back, I just stood by her crib. She saw that I was there, checked periodically, rolled over and went back to sleep. The next night, I sat in the chair in the same room, and she fell back asleep. That gradual approach seemed to do the trick - we got to the point that if she experienced a nighttime arousal, we could address the situation and have her back to bed in a matter of minutes. We also noticed that she seemed to be better at comforting herself if she did awake during the night - evidenced by a few episodes of us hearing her awake, squeak for a moment or two (sounded like she was talking to herself), followed by silence. Overall, the "gradual" method worked pretty well. I hated going back to co-sleeping the last couple nights after making that progress, but I figured her being sick and having difficulty breathing constituted as extenuating circumstances.
I would also recommend the book Healthy Sleep Habits, Happy Child by Marc Weissbluth. The book jumps around a bit and can be tough to follow in places, but does have some helpful advice regarding a child's sleep patterns, and essentially how to help a child "learn" to sleep on their own. Might want to check it out, it helped us!