I'll do my best to answer these, but please remember Lain is a show that leaves most of it's plot open for interpretation. The best thing to do is to rewatch it a few times and try to absorb more information and come to your own conclusions.
To start it's never said the MiB are killed by evil Lain, but Karl is suspicious that the office worker has been in contact with Eiri. It's most likely that he was corrupted by him and sent to the MiB as a messenger before Eiri takes them out himself, remember Eiri's power was at its peak here. The Knights were only a means to an end, with KIDS and the fake Lain they had too much power for Eiri to leave alone. Besides once the Wired was finally merged with Reality we wouldn't need worshipers like them, he would be a full fledged god.
Lain is Lain, there is one Lain. But she exists in everyone; for every memory, every perception of Lain she exists. Her ego seems to reside in Iwakura Lain, but there are traces of her everywhere. Evil Lain works with the knights and is similar to how they seem to see themselves, Wired Lain comes from her interactions in the Wired.
Lain's human form is a bit tricky, but my guess is that it was made by Tachibana Labs. During a quick news segment there's an announcement that they have mapped the human genome, and this was before we actually did it meaning my sci-fi rules at the time they could basically create life. Lain's Father also works for Tachibana Labs, so with that and the Knights watching her it's safe to say they had a pretty big involvement with her.
Her Father comforting her and her disappearance rely more on interpretation, but Lain being considered a Godlike being is in part what started everything; it was the surest way of a successful reset to make that not so.
Lain's sister is also pretty vague, though I think due to the modem noises and her 'communicating' is that the knights were using her to spy; it's not like Lain really noticed anything was wrong with her.