Having trouble finishing his bottles makes me think of two things... he is filling up on water, and he has nasal congestion that is making it hard for him to drink and breathe at the same time.
Sinus congestion leading to heavy postnasal drip can make a kid sound like Darth Vader and really rattly even if their chest is mostly clear (since they are breathing through it- but it's really more up in their throat, not the lungs)...now, with CF in the picture you can never jump to the conclusion that the lungs are clear, but it does sound like nasal congestion could be a big issue worth trying to fix. Saline spray or drops followed by the bulb syringe to suck everything out before it can run down his throat and make him vomit might work better- and don't have him laying flat on his back when you do it (oh it's unbelievable what will come out of that nose!) This can give a lot of relief, even though they will often scream like you are torturing them through the process... Since this has been going on for a long time, worsening, it sounds like the possibility is there for a sinus infection that should be treated.
Back to the water for a minute- did his doctor recommend it? I'd ask about it. If he wants the baby to get extra clear fluids, some Pedialyte might be better, and maybe try it after he's had his formula, so he doesn't fill up on it first.
I hope he's feeling better soon! It's so hard when they are sick