From your second post, it certainly sounds more like reflux & trapped wind than the formula itself.
She has proven to you that she'll take Nutramigen on it's own (even if she hasn't quite comes to terms with the taste of it yet, she'll drink it if she's thirsty/hungry enough which is good).
The wanting to be upright and leg raising was classic reflux & wind with my little boy.
Keep them upright after a feed/meal - on your lap (no bouncing!), highchair/bumbo type seat or car seat perhaps. Have toys they can play with that will keep them sitting quietly if needed.
You can help the wind that is trapped below the stomach by "cycling" their legs (it does involve laying them down, so not too soon after a feed!). I found this helped the bubbles to move along his gut towards his backside, then obviously he'd trump! but at least it was out!
I've had one thought on her other meds. If they are a liquid it wont apply, but tablets might well be coated that often also contains lactose, which kinda defeats the object if they are milk intolerant! Doctors sometimes don't realise all the ingredients in what they prescribe, only what it is for treating.
Thankfully I never needed to try 'flavouring' nutramigen with my LO, but you could try a drop of vanilla essence in the feed, or some cocoa powder (check the label first, some do have milk, others don't). As a last resort, my HV suggested the Crusha milkshake flavouring; but as this would be super sweet, you'd be rotting her little teeth every feed!
Start keeping a diary of what you feed and her reactions, see if there is a pattern to it. This will help the Paeds in January too.
Ask for a referral to a dietician too in Jan, as they can help when it comes to weaning and challenging allergies at a later date.
As littleweed says, you're doing all the right things, just keep going - with a smile on your face when you're feeding! 
If she sees you cringing at the smell, she wont want to take any of it, just smile and stay calm, she'll get the hang of it in the end.