2002 Mercury Sable 3.0l power lost

2002 Mercury Sable this has a lost of power alt to the battery. fuse was blown that was for the alt small 10amp fuse. but anti theft kicked on but lost communication with PCM. port fuse was good changed all fuse relay. on all junction box two under the hood and driver side firewall. key is not the OEM key from Ford. all this started when the alt was changed and car died on the road. new keys was cut but still antitheif kick on. bad PCM or bad key but I can't communicate with anything..