#1 and #2 are very likely the secondary air injection pump components. Commonly deleted before/when they fail because they aren't super cheap to replace, usually, and it's just an emissions component for cold starts, anyways. They likely left that part plugged in so the computer still actuates the valves and thinks it's running like normal. If you look at the back of the heads you'll likely find a block-off plate bolted in (one on each side) that looks like the flange on that part that's just hanging out. I wonder if #4 is some sort of exhaust cut-out you can open/close? Usually people put those further up in the exhaust, though, so I'm not sure why it's all the way back at the muffler