Are you sure this is croup? The reason I'm asking this question is because croup is normally acute and does not tend to last for weeks. If it is croup, the treatment is different than it would be if this is some other type of upper respiratory problem.
Since your daughter is only three and having a chronic problem, I suspect she must have gotten some type of viral pnuemonia in the first two years of her life which has scarred her lungs. Fortunately, they usually outgrow this by 4 or 5, but it can certainly be frustrating and frightening until they do. My 5 year-old had a bad case of RSV, which is a viral pnuemonia when she was a year old. She went into respiratory arrest on me and gave us quite a scare. For the next two years every time she got sick it went into her lungs. I almost lost her one more time due to a bad seizure with a fever. Around the age of 4, she outgrew the problem and has been wonderfully healthy for the last two winters.
Now, as far as how I would handle this:
It sounds like your diet is good - however, when you are on a strict vegan/raw diet, sometimes it is hard to keep the diet as balanced as you would like to, depending on what type of seasons you are dealing with in your climate zone. Therefore, I would use some type of supplementation, especially with a toddler. Look for a good, whole food supplement along with using green drinks to make sure she is getting enough protein, calcium and vitamins in her diet. Then, I would make sure to use flax oil or some type of oil mixture, such as Barleans Essential woman in her green drink or smoothies to make sure she is getting enough of the right kind of fats.
Along with nutrition, there are some specifics I would do to treat the problem. If you really believe this is croup, then you will need to get a cold-mist vaporizer or take her out into the cold night air (make sure she is dressed appropriately to keep warm) to breath the cool air. Croup cannot survive in cold air, so this will help to relieve the symptoms.
If this is an upper respiratory problem, which I suspect it is, I would take her into a hot, steamy shower three or four times a day to help loosen up and move out the mucus in her bronchial tubes. Along with this, I would add a drop of oregano to her smoothie or green drink or bottle, if she is still using one. Orally, I would be giving her 1 to 3 dropper fulls of something like Dr Christopher's Kid-e-well every 1 to 2 hours while she is awake. This is also made by Herbs For Kids and is called the Yarrow Blend.
During the day, I would rub Dr Christopher's X-Ceptic tincture into her throat, chest and back to help fight the virus or bacteria causing the problem and then rub mullein oil over the top of that to help break up the congestion. At night and when she takes a nap, I would probably put Vicks Vapo-rub on her throat, chest and back. I would also make sure I had a hot-water vaporizer going with eucalyptus oil in it to help her breathe better. If you like to use essential oils, there are many different ones you can use in a diffuser, along with mixing them in to some olive oil and applying directly to her chest. When you put them on the back and chest you can use your hand to do what is called, "cupping" to help break up the congestion.
Hopefully, this will help get you started. It sounds like you are doing a wonderful job raising your daughter in a healthy life-style. I would not get hung up, at this point, with allergies or other 'unknowns'.