I'm looking for an older story where kagome goes to the past because something happened to the well an it's putting out smoke. She meets young sesshoumaru in the woods running from some samurai. It has them on a mountain meeting a witch or someone like that also

This sounds a lot like:

The Once and Future Taiyoukai by RosieB

Summary: The well was supposed to be stable. It was supposed to send her to Inuyasha. And it failed. Now, Kagome's even farther into the past and she must depend on a young Sesshoumaru, who has no idea of what their shared future holds. But neither does Kagome.

Rated: T (by FFN.net standards, though it may fall under M or even MA here)

It's been years since I've read it, and I don't recall the story clearly. So, the bumped ratings are just in case.

EDIT: After rereading the story for the better part of last night and early this morning, I'm going to go ahead and confirm that the story should be rated: MA here... due to the graphic nature of some descriptions as well as some of the language used. So, it's off limits for YIMs/minors.