Alabama: apply to UA, UAB (for med-related fields) and UAH (for engineering-related fields) alongside Honors college as soon as they open (typically, early July), then, when/if offered, Honors within Honors like McCollough or Randall Research.
Once those are out of the way, read Fiske carefully or, if you can afford it (time&finances-wise) go visit a variety of colleges that run the gamut in terms of vibe but offer an excellent education in STEM: beside those you listed, what about Smith, Brandeis, WPI, RPI, Skidmore, W&L, Davidson, W&M… Take advantage of the summer to visit. You could organize one “NYS/MA” tour and one “NC/VA” tour, with one short trip to Atlanta added during Fall Break 
(though you’d have to be sure about Engineering if you chose GTech and being premed if choosing Emory.)
It’s difficult to chance you on your reaches individually but in aggregate I’d be surprised if you didn’t get into Case Western EA for Engineering plus 1-2 others and if you like UA Honors then you’re set. 
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