95 Protege electrical problems. Need advanced help

I have a 95 Protege DX. I installed two 12 inch subs and an amp @ 500 watts rms. The system was causing my headlights to dim so I put in a bigger battery. Battery is an 880 cca farm and fleet platinum. I also upgraded the alternator to a 140 amp HO from ace alternators. On the first drive with everything installed, out of nowhere all the electronics went crazy like they were getting way too much voltage and the car died. So far I pulled the ecu and removed the cover and the board was charred. The harness also has charring. To my knowledge the alternator shouldn't put out more voltage than is being drawn and it tested fine on a bench test so I have no idea what the underlying cause could be. Ecu? Power/ground wires? Any help is appreciated because I need my car back asap

First off, with only 500 watts you shouldn't need any electrical upgrades... Dimming is a matter of physics, they will always dim a little no matter what you upgrade in the system. Did you do a voltage check to see how far it was dipping?

The HO alt could have been regulated differently or had a faulty regulator causing it to overcharge.. They can produce 18+ volts pretty easily. Did you do a voltage check at the battery with the car running after installing the alt?

The alternator will only produce as much current (amps) that is being drawn. Voltage should stay steady around 13.5-14.4 volts.