Yes, having low stomach acid makes it difficult to digest protein and yes, that will make you bloated. I get really bad belching when I don't take hcl with protein.
Okay, so I take 1800mg/ meal. I've found that there are generally two sizes for hcl: low dose (like 200 or 300mg) or high dose (like 600 mg). I use the 600mg so that I don't have to take so many pills.
The below article explains one way to go about figuring out how much to take. Personally, I like to take my hcl with meals, as apposed to after, like she suggests.
Good luck! You are on the road to eating protein again. Wahoo!!!