Windows/gauges not working properly

It started with my key fob not working. When I would open the door with the key the alarm would go off but usually you stick the key in the ignition it would stop. This time I had to unhook battery. Changed key fob battery still doesn't work. The next day go to leave start vehicle up and none of the gauges are working. All lights in vehicle on, power windows not working. Let it sit for a day come back to it and now all the gauges are working. Check engine light is still on but no windows working. Checked all fuses everything is good. Hooked a computer to it and all it says is it needs fuel injector #6 and that's already been taken care of. Please help!