Try to wrap that all up in Chapters 2, 3 and 4. You can do it later, but it starts to feel completely antithetical to the narrative later on. There are some sidequests that only exist in Chapter 6, to be fair; apart from that, get them done sooner rather than later.
Three per day. Take them, sleep for 18 hours, eat something (you don't want your weight to start dropping off), take another dose of tonics, repeat. There's a chart, which I think is still accurate:
This is a common complaint with the game. I didn't have this issue at all on my first playthrough; on my second, it happened to me more than once. It's annoying, but the loot you get is almost always pointless anyway. Oh goody, 2 dollars and some chewing tobacco. Almost useless. Don't worry about loot in missions; before long, you will have an abundance of money, ammo and tonics regardless.