Wow; I'm so sorry. It sounds like you've got a lot going on. I'm sorry about the health of your little one too; hopefully he'll grow out of all of his troubles.
I have a ten-week-old (and he's my first) so I definetely don't have much experience; however, my little guy has awful reflux as well. He's been on Zantac since around four weeks. The Zantac removes the acidity of the vomit/spit up in his throat, but he still throws up frequently. We found that if we hold him upright for 20-30 minutes after he eats it helps a LOT. We also raised his crib matress so he's sleeping more upright on an angle. This has helped as well. I wish I had more ideas; you've probably tried both of these-but, just in case you might want to give them a shot.
Is there someone that could watch your little one so you can have some free time with your toddler? I once read a good quote about spending time with kids. As much as infants need all of our attention; it's the toddlers and school-age kids that are going to remember if we were there for them once the younger sibling arrived. The infant won't remember; so if your toddler needs some time; leave your infant for a bit and focus on the other sibling. He/she is probably having a rough time too.
Good luck; I hope that things start looking better for you.