Half the fusebox in engine bay not working

I was changing out the alternator today while I was putting everything back together, without thinking, I hooked up the negative wire back to the battery to open the trunk. I quickly removed it when I realized the hot wire that is bolted to the top of the alternator was actually touching a small bolt on the black cover of the alternator! Now my starter, radio, rear electrical systems(lights, trunk release, trunk light), aren't working and even my obdII port won't respond to the scan tool. Also my key won't open my doors. Only the remote will. I checked the fuses with a voltmeter, none blown but some are receiving no power. My dashboard info still shows, my front headlights still work though. Could you give me an idea of where to check next, what the problem might be? I'm ashamed to say this isn't my first alternator job but any help would be much appreciated. Thanks! (In the picture, the circled bolt is what the hot wire touched.)