How old is she? My daughter had day/night confusion for the first three months of her life...it was awful! Also, she seemed to be awake all the time and only napped in 20 minute increments! But when the three month mark came she turned into the "perfect" baby, sleeping for 5-8 hours a night, taking 3-4 naps a day, I could actually PLAN things!
Here's what I think: the reflux is playing a big part in her not having a schedule. She can't sleep well because of the reflux and that is "throwing off the works." Also, I wouldn't advise you to WANT her to be awake at 3 am, no matter that that's when your husband is home, because ultimately in a few months you won't want that for her. In my experience (degree in Early Childhood Ed. 10+ years working with children, mainly infants, and mom of one 5 year old girl) by the time a baby is about 6 months old they should be on a general schedule. Trying to get them on one before they are ready will only make you frustrated. Most babies develop some sort of schedule around these basic parameters: waking in the morning sometime between 6-8 am, napping in the late morning, napping in the mid to late afternoon, maybe catnapping in the early evening, and going to bed somewhere between 7-10 pm and sleeping pretty much through the night, possibly waking for a brief feeding then going right back to sleep.
I just talked to my sister yesterday, she has a 6 month old and is having some trouble with feeding and I told her this: it seems like it's never going to end but just remember that in 6 months your baby will be 1 year old and all of this will be a distant memory. Do what you can to get through it, try to watch your baby for cues so you can get her on a schedule, and just remember that babies change quickly. Just when you think you have a schedule or pattern, she will change it! Good luck, let me know if you need any more help, keep us posted!