I didn't have the time to read every post, so forgive me if I repeat what has already been said.
Adding a bigger alternator will not harm your electrical system. Your voltage is not changing. It's just the amperage supply that is changing. You can add a 1000 amp alternator to a car, and as long as it's still supplying no more than 14.4 volts, you'll be just fine. An alternator's amp output is just a supply, meaning it will only supply the amperage needed up to that rated amperage. Your electronics are not in danger. You can run your car for the rest of it's life without doing the big-3. However, If you are referring to your audio system needing that extra amperage, then you would only need the big-3 for your system, but only if you plan of cranking the system past the limits of the wire.
I apologize if I don't make any sense. Maybe I should have Mitchell explain it for me. LOL....