Couple of points, maybe you've already thought of them:
- What accessories do you have that would require a 100 AMP alternator? Have you calculated on paper what your total load would be with everything turned on? Maybe there's a short somewhere and that's why your alternator is working so hard? Just guessing but 75 AMPs seems like more than enough for a typical cobra with minimal accessories.
- Yep, you need a master fuse on the feed wire from the alternator for the reason cited. Voltage regulators go bad quite frequently and you need the fuse to protect the wiring, your battery, and the main bus.
- Fuses protect the wire, not the device so size your main fuse accodingly. You don't really need to go much larger than 20% larger than your maximum alternator size.
- For a 100 AMP alternator, you may need a 2AWG or 4AWG wire depending on the length of the run. I like to use welding cable from a local source. They usually crimp the ends on for free. The fact that your insulation is discolored points to the wire getting hot. Maybe it was just from the alternator overload but maybe it contributed to it as well as resistance goes up with the temperature of the wire.
- Sealed batteries like the Optima require different kind of trickle charging to keep them fully charged for anything not used on a regular basis. Not keeping them charged and not trickle charging them properly results in shorter battery life. Unless you race, you may find the performance from a wet battery to be more cost effective the next time you have to replace that Optima.
Like all advice, it's worth what you paid for it. Hope you get things up and running quickly.