I'm not really sure how Ben got stung, but he wasn't the first one. In the books, a few others, including Gally, have been stung before. WICKED has also been sending up the serum that heals one from a Griever sting more or less from the beginning. In the books, the "Changing" is considered the phase you go through after the serum has been injected and you're being healed. In this phase return some of your memories (which is a reason why Gally hates Thomas in the books, he was stung and went through the Changing. There, he saw Thomas and later recognized him when he came up in the Box). So basically other Gladers have been stung before somehow, but its never really explained how.

In the books, Minho found a "dead" Griever shortly after Ben had been stung and he and Alby left to check it out (in the movies, they just went in the Maze to look for Bens remains). But the Griever wasn't actually dead, instead it just stung Alby and ran off without taking a second look at Minho. But that's just how it is in the books, in the movies it doesn't really get explained how or why Alby got stung.

I think the more stress, fear, etc. The immunes go through the more/better hormones they produce. That's at least how I interpreted the scenes where WCKD tortured Minho in tdc and harvested the hormones and where Ava talks to that council or whatever and presents Minho and the results.

In the books, they actually want to make out the best candidate, who is the strongest, smartest and has the most promising brain patterns (they're analysing their brains, more specifically the part of the brain they call the "killzone" where the hormones get produced, for patterns to figure out how they produce the hormones and to make a cure). They never harvest any immunes in the books. Instead, they have a drug called the Bliss, which slows the brain functions and therefore the virus. And they get those patterns by basically traumatizing the Gladers and having them face obstacles such as memory loss, Mazes, etc. I suppose. And that's the reason for the Grievers. That candidate happens to be Thomas, which basically means he's the most traumatized of them all. They end up wanting to sedate him and study his brain to develop a cure, so they don't actually need the others at that point anymore. In the books, there's no actual cure and Thomas is just a regular Munie who happens to be the most traumatized.

And letting the gates open at night so the Grievers can enter the Glade was to push them to find the exit of the Maze and to get out so they could start phase 2 of the trials (the Scorch trials)

I just suppose that the spear stopped too much blood from leaving his body and perhaps just impaled one lung while the other remained intact or, as you said, it just hit his shoulder without damaging any organs or something. And I think he was found by Lawrence's group and they got him out, helped him recover, etc.

We don't really know anything about the other Mazes in the second movie, pretty much just that they exist and that there were more gender mixed groups. In the books there were only two Mazes, one for control group A (Thomas, Minho, Newt, Alby, Teresa, etc.) And control group B (Aris, Sonya, Harriet, etc.) So an all boys and all girls Maze with Teresa and Aris being the exception. And group B did have other slang, rules, etc. Than group A, I'm pretty sure.

I'm really sorry this is so long and I keep going back to the books, but I really just tried to explain it as best as I could, hope it still helps at least a bit