My suggestion is for the neb treatment. My daughter was diagnosed at 2 with Asthma. She hated the fish mask with a passion. Screaming, crying, the whole nine yards. They do not have to wear the mask. They do just fine with the regular attachment. If she has to have another treatment make sure you tell them you don't want the mask.
I'm thinking she saw something on tv where something or someone went down the drain. Sounds a little like Finding Nemo? Lots of kids have that phobia. Try filling the bathtub and putting some toys in there. Bring her in to the bathroom and drain the tub while she is standing there. Show her that the water goes down the drain but the toys stay in the tub. Explain that if the toys, which are smaller than her brother, do not go down the drain, a person could never go down the drain. Try to make bathtime more fun. Try bubbles. Buy some bubbles and instead of using them outside, use them in the tub. They love that. It's a little messy, but your in the tub, so who cares. Watch your floors, they become slippy if the bubbles spill on the floor. If all else fails, know that she will grow out of it.
As far as naptime goes, she might be afraid, now that she has a little brother, that she is missing something if she does not nap. My oldest went through that when her sister was born. She really needed a nap, so I started offering treats if she would just sleep for one hour. (always slept longer) When that stopped working, we would play a game (just the two of us) when she woke up, if she would go to sleep. When they are at that age they need a routine for their naps. As hard as it is when you have running around to do, you need to have nap time at pretty much the same time every day. After lunch is always good. That way she knows, lunch is over and now it's time for my nap. It might be hard if you are use to running around during the day, but if you really want her to nap, do your running around in the morning. Once you start the routine, she will automatically know, lunch is over, now I am going to lay down. Start that now because it is very hard in the summer to start a routine like that. Routine really is key for nap time.
Good luck!