My grades throughout high school have improved from mid-90s (freshman year) to an overall 98 average in junior year. We dont do 4.0 scale. In senior year, my first two quarters are back to what it was in freshman year, except im taking all APs this year and none during freshman year (my school doesnt offer it that young). Since I “dropped” my grades back to mid-90s, will that look weak to extremely selective colleges? (ivies, northwestern, washu etc.)
Only on College Confidential will students think that a drop to the mid-90’s is problematic. 
No, it’s fine. It’s also common. The material is harder in 12th grade vs 9th (or even vs. 11th), and the grading is generally tougher. Wait until college - the grading metrics only get more severe. Good luck.