I do not think that Stanford cares about freshman year grades. Universities in Canada do not consider freshman year grades, although I suppose that on a worldwide basis Toronto and McGill are not quite “top 20” (Toronto is close in some ratings).
The Ivy League universities (and Stanford) are going to be reaches regardless. You have VERY good in-state public universities in California. As others have mentioned, for engineering you would probably be better off at UCB, UCLA, or Stanford compared to the Ivy League schools, although bioengineering is sort of special and different universities might be best in this area.