Let's see if I can answer those...
1) Since they already time traveled at least once (original time line), then yes, Janus and the Gurus will doubtlessly appear in their respective times.
However, since the ones to appear will be the ones coming from said original time line... Well, look below.
2) Having Zeal surviving means that history suffers a very big change. Considering how both the Enlightened Ones and Earthbound Ones had to live together now, by 600 AD (or even way before) everyone already has had both as ancestors. So in the case Zeal continued to live on floating in the sky, then it means no Cyrus, Glenn, etc.
Then, Zeal was the cause of the endless blizzards that were present since it rose. By continuing to float, the blizzards will keep going, preventing the Earthbound ones to live above the surface, meaning no Guardia, etc.
3 and 4) Since Lavos was the cause of both, then by it's defeat, it means Zeal stops being both.
5) Lavos wasn't the only source of magic. The Enlightened Ones used the planet as their source, like the use of the Sun Stone, before finding the Frozen Flame. Besides, when Zeal fell, they only lost their ability to use it, they still had it, so doubtless that they can still use it after Lavos's defeat.
6) Since it's highly likely that magic won't fade, the islands could still float. Though I'm not entirely sure of this one.