I'm about a year ahead of you in this journey. I was there last year and I'm there now as far as the eating etc. stuff goes. I could have written every word in your post last year.
first thing I did was talk (not at meal time) with my two boys about how the rules are different for their sister. Whenever they complain that its not fair that she gets dessert without finishing her dinner, I remind me them that lots of things aren't fair. We discuss that Alyssa needs to gain weight and she has to do a lot of things that they don't: like meds, her vest, nebs, etc. and that the rules are just different. I let them express their frustration just like I let her express her own for having to do all those things "normal" kids don't have to. It sucks for everyone, but its the way things are.
My best advice on the food front is try to make offers for foods that are calorie dense. So instead of trying to get quantity in (which can be impossible with a picky toddler) make it quality. I got a can of duocal from our nutritionist and so whatever I could get my daughter to eat I would boost the calories with butter, duocal, heavy cream, etc. I also try to give her a variety of foods ont he plate. I don't expect her to eat everything, just figure that whichever she chooses will be good calorically. Even veggies get drowned in butter and/cheese bacuse it just figures that she would prefer broccoli to the calorie laden mashed potatoes. But you do what you can.
I have to say, that about 3 months ago, I just let go a bit. I was so done with the misery her meals with creating for me. I prepare the best meals I can and I try not to sweat it. We have three scheduled meals and two to three scheduled snack times. So if she doesn't do well on one, I just try again the next time. I can also get two cans of pediasure in a day, both right before she goes to sleep (nap and night).
All in all, we do the best we can and she still struggles to gain, but we are doing the best we can.