Lynsey,
CF and reflux are VERY common. This is actually how much daughter, Hayley, now 2½, was diagnosed with CF. She was not gaining weight and had severe reflux, our family doctor put her on Zantac and it was not helping, so he referred us to a pediatric GI and the day after we met with him, she started aspirating her formula. Very scary! I was in the middle of Meijer's shopping ans she was in her infant car seat in the cart (she was only 3 months old) and she started turning blue and gasping for air. We were admitted and she eventually ended up on a venitlaor and everything. They also did the upper GI, which showed severe reflux and then a bronchoscopy, which confirmed she was aspirating formula into her lungs. She ended up having to have a Nissen Fundoplication (stomach wrap) just Google, "Nissen Fundoplication" and you will get a better explanation of the surgery. It does cause problems for some after the surgery, but Hayley has done really well and not had any complications from the Nissen. Basically it wraps the stomach so nothing can come back up the espohagus and out, so she cannot burp, vomit or anything.
Then after the recovery from the surgery we went home thinking everything would be fine, only to return to the hospital the next day because she was still having a difficult time preathing and sounded horrible. They admitted us again and did the sweat test and that's how we found out she had CF.
So if you have anymore questions ask away, but I would stay on top of this and do all the testing your doctors recommend! Good luck!