'94 Cherokee battery problem

I have a 1994 Cherokee, everything died (ac, wipers, radio, turn signals, except the head lights) now the battery light turns on, and the battery is not recharging, so the car dies after a couple of days. I had the altenator and battery checked and are good. Does anyone know if there is a main fuse/relay that I need to check, I checked all fuses and all are good. All these problems started when my key got stock in the ignition while the car was on, so I disconnected the battery to turn the car off, and it didn't turn off, so I pulled out the engine relay. Someone said that I burned a computer in the car when I pulled out the relay. Can someone please shed some light?