If a brake light bulb has been replaced and doesnt match the resistance of the stock bulbs exactly then that light on the dash will come on...the lights will still work but but the dash indicator will still come on when the pedal is pressed.

The stock blows (Bose) radio is garbage it could just be shot

For the misfire do a power balance test to find the bad cylinder...unplug one coil pack at a time and listen to the idle drop, when you unplug one and it has no effect on the idle then that is the bad cylinder. Once you find it ohm the injector, should be between 11-13 ohms. If that is ok then check the coil, swap it out with one from another cylinder, if the misfire moves to that cylinder then thats your problem. If the injector is good and so is the coil then check compression

If the misfire comes and goes with the check engine light you could have a corroded connector or bad wire

To check the ECU codes pull up the passenger floor board and get to the ECU, there is a hole in the side with a little dial, turn the dial clockwise for 2 seconds and then back, the check engine light will flash. The first series of long flashes is the first number followed by a series of short flashes which is the second number

Ex....5 long flashes followed by 5 short flashes would be a code 55 which means all clear

For detailed instructions with pictures and ECU codes go here ECU diagnostics