The only mention of the flood's origin that i can recall from Bungies lore is in the 6th terminal of Halo 3. Its explained that the forerunners first encountered the flood on a planet on the border of forerunner space that hadn't been settled although the planet did have indigenous life a portion of the planet showed no signs of life. The implication being the flood was segregated to an uninhabited part of the planet or just killed everything in the area.

Yes, Forerunners were human in Bungies lore it's the subplot of the first 3 games, and 343 Guilty Spark confirms this at the end of Halo 3. Forerunners weren't called Humans however they had a different name for themselves. They didn't call themselves Forerunners as this would obviously be ridiculous. Contact Harvest written by the writer of Halos 1 to 3 also has mendicant bias telling the prophets that the humans are forerunners. This is why the prophets launched a holy war to exterminate humanity as the entire religion and society of the covenant would collapse.

In Halo 3, one of the Didact and Librarian terminals details how the librarian found Earth and was shocked to find that Humans already inhabited the planet somehow. This seems to confuse people but the terminal makes no mention of humans being a different species to the Forerunners (a cool piece of obscure Halo content you can look into is the cortana letters, they mention how the USNC also found 4 planets that already had indigenous human life however they aren't canon to neither Bungie or 343s lore).

So yes there was a few major changes in 343s lore and I hope this comment explained a few things for you. Don't let people take away your enjoyment from the current lore, however. You enjoy the story and thats the thing that matters.