Gonna only be one of a handful of things, in order of probability:

1) Bad alternator. Meter across the top of your battery or the alternator when the car is running; you should get 14.2-14.6 volts. If lower than this, your alternator (or one of its subsystems, see below) is bad.

2) Bad battery. I always thought Optoma was the best, but my last battery of theirs was a dud. Your local autozone can check this. This is actually super-difficult to troubleshoot at times, as you'll still get 14v on it when the alternator is running, and might even have mid-13's when not being charged.

3) Bad alternator belt. Belts slipping are fairly noisy.

4) Bad ground. The ground for a 4Runner battery is tiny and corrodes easily. See where the ground from the battery goes into the frame and that it's affixed properly.

5) Bad starter contacts. This is a known issue on the 4Runner, and can cause hard starts and consume considerable amperage. But it doesn't explain the other faults in your electric system.

I'd recommend checking the battery (drive to Autozon with a wrench, pull it, bench test it). If the battery tests good, new alternator and belt; if bad, new battery.