As far as the "9/q" thing... I think it's actually written out on the letter to Snake, so Zero never actually says it's a "9" at the end. It was written in the letter at the beginning, so if anything Snake kind of flubs it.
The thing here is that the original puzzle in Japanese was more phonetic... they used the Japanese word for 9 "ku" which has a "kyuu" sound, so the 9/q thing would work easily. If I recall correctly the translation team switched it up so that it was written (so the mixup would still work logically), which is actually extremely elegant and a great job by them.
Zero was Akane with help from her brother.
It's been a while, so I'm rusty, but here goes as far as the last explanation: What was happening was that in order for young Akane to survive, she needed the answer to that last puzzle. So in order to get the answer, she had to create a situation where she could communicate with somebody through the morphogenetic field, which means she needed to set up the Nonary Game. You'll notice that during the game when Junpei makes decisions which jeopardize the "true" ending, June starts to get sick/feel feverish and, near the end, disappears completely. This is because you're playing a timeline that doesn't save her, so she can't exist.
So what was happening when you played the game actually WAS playing alternate timelines. Each ending was an individual timeline that Akane was exploring until she found one that resulted in her being saved by Junpei.
As far as the rest of the stuff, VLR covers some of it so I won't say anything else
Enjoy!