I got B+'s in Spanish III Honors, English II Honors, and Chem Honors, as well as Comp sci and Journalism this year due to some personal issues. Will this affect my chances of getting into selective colleges? My schedule for junior year is Physics Honors, Precalc Honors, English III Honors, AP Spanish, APUSH, AP Bio,and AP Psych. If I get all A’s this year, will I be able to make up my shortcomings 
My freshman EOY grades were all As…
It sounds as if you are doing everything you possibly can to ‘make up your shortcomings’. Obviously your GPA is permanently damaged, but all you can do now is get it as high as possible. Also, the big thing on college applications now is community service hours and how involved you are in clubs, so think about those too!