Hello and welcome to the site!
There could be a lot of things going on with your dd, from teething to needing a change in her schedule. I'd suggest you to look at the FAQ section of this board under a thread called Most Common Sleep Busters to read through it and see if something rings a bell.
You mention she's been sick for over a month (or at least, still has a cough) it must've been a nasty virus, and teh vomiting is totally normal, as long as it is not at every meal. Sometimes it's the phlegms that are stucked in the throat that stop the food from "sliding" and then they vomit because of it. Sometimes is the antibiotics that upset the stomach. I'd suggest you to try with soft meals such as fruits and steamed veggies and leave the protein intake to milk and cheese. She'll get a chance to eat better and more variety when she feels better.
As for the night wakings, as i mentioned they could be due to a lot of things, you can try to reduce or improve them by placing a humidifier on dd's room (to avoid so many coughing episodes), elevate her mattress toa 20 degree position, to avoid phlegms to come up and cause more cough, use decongestant (approved by ped) before bed. But still while she feels poorly and then a couple of weeks later, is perfectly normal for her to wake at night and need some extra reassurance. Remember she's still really young and doesn't understand what's going on so added to pain and stuffiness there's the extra stress of being sick and feeling down and don't understand why is this happening to her, so she calls mama to feel better. Give extra cuddles during the day and as long as she's not crying hysterical or waking for other than cuddles, go with it. I think you're handling great the night wakings and suggest you to keep at it while she's ill.
HTH and post back if you have more questions. Get well soon!