not charging correctly 2013 49,000 miles

Ok i made a big mistake. In trying to hook up a compustar cs 7900 remote start and alarm. I was sold the wrong T harness when i hooked up the power cable the key was in ignition the truck started. Yes i know i should had disconnect the battery. But it blew the fuse on the obd2 connector. The abs and brake light are on and it wont come out of park. I replaced the 7.5 fuse for the obd2 i have the reader and it tells me not charging enough. I just bought the truck and the alternator guage i thought was always low .like a quarter way under 12 not sure if this was normal. But i did i damage the alternator? Is the voltage regulator inside the alternator. What else to check. Thanks for any help . Ok i found and fixed that problem now i have lost communication with the 4wd clutch control module any suggestions where to look on that one uo114 is the code

 

neutral safety switch may be damaged, due to the brake light being on and not coming out of park... You may have to pull all fuses out to test them individually and ensure they are good.... You may need to have the body control unit tested to ensure it functions properly....

 

I fixed that issue it was a couple fuses. Thanks