There seem to be a lot of confusion about Junko's backstory, so maybe this would help a bit. After some digging around at some Chinese forums, the story basically goes like this.
[Warning: there will be a mix of original myth and zun myth]
The original tale of Junko or Xuanqi, goes something like this. She was originally the daughter of a lord back in ancient china, but one day while outside, the xia dynasty emperor, Houyi, was attracted by her beauty. He then forced her to be his wife and killed her son, Bofeng, these all greatly angered Junko. So she teamed up with HanZhuo, one of Houyi's more ambitious subjects, and planned to kill Houyi and make HanZhuo the emperor. So for years they began secretly teaming up with all of Houyi's subject, until all of the people around them are part of the plan (Which was very easy considering Houyi was a tyrant and a shitty emperor). So one day, after they got Houyi drunk, they killed him and the rest of his family then made HanZhuo emperor. In the end, Junko got her long time revenge by chopping Houyi's dead body into little pieces and forcing his sons to eat his flesh.
As for Chang'e, everyone know the story of the Houyi who shoot down the ten suns and Chang'e was that Houyi's wife. There are some additional bits that is more obscure, the bow that Houyi killed the ten suns with was given to him by DiJun he gave it to him for him to maintain peace of the land, but ended up killing DiJun's sons (the suns). For this Houyi was stripped of his power, but XiWangMu took pity and presented to him the immortal medicine, however the medicine were all eaten by Chang'e and Houyi was left to die on earth. (In some version Chang'e regretted this decision, in others she didn't)
It gets even more weird when you consider the ten suns relationship in all this (Involving XiHe), but that is beside the point. It is a very confusing myth/history, cause it is confusing, China didn't have a very good record of this period of time and any reliable pieces got burned up in the cultural revolution.
Now for ZUN version, which is basically a mix of the two.
Houyi was the hero who shoot the ten suns (killing apollo and 8 other sun gods) and was very high-classed, he had two wifes, Junko and Chang'e, he also killed Bofeng, the child he had with Junko. As for the reasons for him killing Bofeng, no one knows, there are a group of Chinese fans who are digging around ShanHaiJing and coming up with a couple possible explanation (ranging from him choosing Chang'e over Junko to more outlandish explanations). The fact is he did it, and Junko hate him for it, the rest went like the myth, she killed him, in fact she killed him so thoroughly there were nothing left of his soul. But Chang'e went back to the moon before Junko could make her pay for her part of Junko's lost (which is surprisingly, a lot). And she have been pissed off ever since.
The more interesting bits are when you dig around this mythology, I would say this is one of the more interesting myths to dig around cause it makes the entire thing more of a mess.
- First interesting bit, in Houyi's sun shooting myth, according to ShanHaiJing (or some other Chinese myth book), Houyi shoot down the suns under the direction of what could be the Celestial Bureaucracy, the ten suns were sons of the goddess XiHe. Which is hilarious when taken in Touhou term, meaning Apollo was the son of XiHe, not sure if Zun realise it or not, but it makes for a pretty hilarious neta.
- Second interesting bit, depending on which version, Houyi was either worshipped as a hero, or greatly punished for his action. In Touhou version, it boils down to the Celestial Bureaucracy seem to be happy while the other aboriginal myth gods are pissed off at him (such as Hecatia). Seem to be more Central Mythology vs Aboriginal Mythology.
- Chang'e was the wife of DiJun, who is also the husband of XiHe. Dijun was also Houyi's boss in ShanHaiJing. The part where people say that Houyi shooting the suns killed Junko's son, was probably a mistake in mixing XiHe and Junko. Which is understandable cause Chang'e married both of these mens, it also have something to do with the source of XiHe and Junko's myth, but the records gets way too fuzzy at that point.
- Another interesting bit about ZUN's version of Houyi is that he is really really REALLY died, otherwise Junko and Hecatia wouldn't be going after Chang'e.