Electrical problem after running a bad alternator

Check for blown fuses under the hood, and inside the car.

Which Civic do you have? CX, DX? Looks like eight different versions for that year. Also appears to be close to ten fuses for the windows and dash. It is also possible it is a ground but need to know exact vehicle for that. Thanks.

Under the dash is a power window relay. Feel if that clicks when you turn on the ignition switch. If it does, at least one of the passenger windows should work. If it does't click, there is a blown 7.5 amp fuse # 6, also under the dash.

How about a circuit test? Go under the hood and locate the power window fuse in the fuse box on the passenger side. Check it with a test light for voltage on both sides. Now locate the White with Blue stripe wire coming out of that box and check it for power. Next find the relay under the dash and check there for 12+. Turn the key on and check the individual fuses 7, 8, 10, 11 in the under dash fuse panel. If you have power to them the relay is OK, The most likely suspect is a failed master switch.

For the dash lights, Fuse 30 powers all the illumination lights, dash, shifter, heater so if the other lights are working the issue is probably the dimmer control or the dimmer circuit in the dash.

If you find 12 volts on a wire to a window motor, check the other wire too. If you have 12 volts on both wires at the same time, regardless which way the switch is pressed, you are missing the ground circuit. The best suspect for that is a broken wire between the driver's door hinges.