Brake light comes on/of, air conditioning turns off and on, lights flicker, power doors and windows lose power on & off, beeping noise, clicking noise in the glove box horn honks all while driving

Engine compartment

Toyota Matrix - fuse box - engine compartment

Instrument panel

Toyota Matrix - fuse box - instrument panel

Fuses (type A)

Fuse Ampere rating Description 1 FOG 15 Front fog lights 2 HEAD LH UPR 10 Left?hand headlight (high beam) 3 HEAD RH UPR 10 Right?hand headlight (high beam), high beam indicator light 4 SPARE 30 Spare fuse 5 SPARE 15 Spare fuse 6 SPARE 10 Spare fuse 7 ETCS (1ZZ?FE engine with two?wheel drive models only) 10 Electronic throttle control system 8 AMP 30 Car audio system 9 MAIN 30 Starting system, "AM2" fuse 10 DOME 15 Car audio system, clock, personal lights, interior light, trunk light, open door warning light, wireless remote control system 11 HORN 10 Horn 12 HAZARD 10 Emergency flashers, turn signal lights 13 EFI 15 Multiport fuel injection system/sequential multiport fuel injection system, emission control system, "EFI" fuse 14 ALT?S 5 Charging system 15 HEAD LH LWR 10 Left?hand headlight (low beam) 16 HEAD RH LWR 10 Right?hand headlight (low beam) 17 EFI2 (1ZZ?FE engine with two? wheel drive models only) 15 Multiport fuel injection system/ sequential multiport fuel injection system, emission control system 18 TAIL 15 Tail lights, license plate lights, instrument panel lights, instrument cluster lights, clock 19 OBD 7,5 On?board diagnosis system 20 WIPER 25 Windshield wipers 21 AM2 15 Charging system, multiport fuel injection system/sequential multiport fuel injection system, starting system, SRS airbag system 22 STOP 15 Stop lights, high mounted stoplight, anti?lock brake system, shift lock control system, multiport fuel injection system/sequential multiport fuel injection system, cruise control system 23 DOOR 25 Power door lock system, glass hatch opener switch 24 AM1 25 "CIG" fuse 25 ECU?IG 10 Electric cooling fan, anti?lock brake system, traction control system, vehicle stability control system, brake assist system, shift lock control system, cruise control system 26 RR WIPER 15 Rear window wiper 27 A/C 10 Air conditioning system 28 INV 15 Power outlet (115 VAC) 29 P/POINT 15 Power outlet (12 VDC/ in the rear console box) 30 ECU?B 10 Daytime running light system 31 CIG 15 Power outlet (on the instrument panel) or cigarette lighter, car audio system, clock, power rear view mirror control, shift lock control system 32 GAUGE 10 Gauges and meters, air conditioning system, daytime running light system, charging system, auto anti?glare inside rear view mirror, power windows, cruise control system, rear window defogger, back?up lights, front passenger's seat belt reminder light 33 WASHER 15 Windshield washer, rear window washer 34 M?HTR/DEF I?UP 10 Engine control system

Fuses (type B)

Fuse Ampere rating Description 35 ABS NO.1 30 Anti?lock brake system, vehicle stability control system, traction control system, brake assist system 36 RDI FAN 30 Electric cooling fan 37 ABS NO.2 40 (without vehicle stability
control system) Anti?lock brake system 50 (with vehicle stability
control system) Anti?lock brake system, vehicle stability control system, traction control system, brake assist system 38 HEAD MAIN 40 "HEAD LH UPR", "HEAD RH UPR", "HEAD LH LWR" and "HEAD RH LWR" fuses 39 AIR PUMP 50 (1ZZ?FE engine with four?wheel drive models and 2Z ?GE engine only) Emission control system 40 HTR 40 Air conditioning system 41 DEF 30 Rear window defogger, "M?HTR/DEF I?UP" fuse 42 POWER 30 Power windows, electric moon roof

Fuses (type C)

Fuse Ampere rating [A] Description 43 ALT 100 Charging system, "ABS NO.1", "ABS NO.2", "RDI FAN", "FOG", "HTR", "AM1", "POWER", "DOOR", "ECU?B", "TAIL", "STOP", "P/POINT", "INV" and "OBD" fuses WARNING: Terminal and harness assignments for individual connectors will vary depending on vehicle equipment level, model, and market.

check the abs system for relay and electrical problems
the clicking can be from a cycling relay and the head lights flickering from the power draw for the abs away from the head lights.

I believe those older cars used circuit breakers, not relays, for the power window systems. By using a test light, you don't know if battery voltage is present at the window switch. Maybe the voltage is reduced, somehow.
I would first check the switch's power with a voltmeter. If the motor is getting battery voltage, I would say the motor. If the voltage is low,
you had better find a wiring diagram, Dave, to trace it out.

Check and possibly clean all connections to the battery(bat clamps/posts)...check to be sure the ground on the block and the body are clean and well connected

Sounds like u have a set of crossed wires.most likely your brake lights and your indicator lights. as for the beeping. could be another short ti power for your door dinger. this is assuming that the beeping is the same as if u left your keys in the ignition

sound like you have a lose connection it could be the cables on to the dash or the socket it fits to. you would need to remove the dash and clean the connection and re fit it. if you push on the dash does it stop. ? just check this first as some times its just a tiny amount of play in the connections that's the problem .

clean the baterry cables

You diffenently have a positive wire grounding out somewhere

CHECK ALL FOUR DOOR LIGHT PRESS IN SWITCHES FOR A LOOSE WIRE OR BROKEN.