Car is an '08 type S 6mt

I changed my alternator a few weeks ago. Was driving, car died, got car home. First of all, yes I unplugged my battery to start with. It needed to be charged anyways so it was completely removed from the car. Now, I replaced the alternator, made sure all connections were secure etc. Then I reinstalled the battery. After getting everything back running I noticed my radio wasn't working. I proceeded to check all the fuses(cabin and engine bay) and I noticed almost all of my 7.5 amp fuses were blown. I replaced everything that was blown and everything works EXCEPT my HID will not switch to high beam. The fogs turn off, but the cut off shields do not move. What should I check next?

Thanks,
Cameron