I've reached only as far as Chapter XXIII in my reading/recording of
Roughing It and it's been more than a couple of decades since I
previously read this book all the way through but I can't recall any
mention of Mark being personally attacked by Indians.  As for the
Goshoots, his reaction was based on their appearance as seen around the
stations and the stories he heard of them from fellow travelers.

I still suspect that his main difficulty with Indians, at least Western
Indians, is that they were as culturally removed from him as anyone he
had ever met or would ever meet.  He could not reconcile those
differences with his own sense of values.  Consequently, they became
sub-human, brothers of the cayotes and the ravens. Scavengers and
harvesters of offal.  And, murderous cowards to boot.

It would appear from reports following the thread that we developed no
more real interest in them other than the Indian Wars.  But this would
no doubt be in relation to the American heroes that did battle with
those Indians.