Electrical Nightmare, Grounded out my alternator Options

[[Freemantle]]

I was having one of my friends figure out where in my drivetrain this loud ticking noise was coming from (cracked lifter on an intake valve in #1, this is another day's nightmare).

When he was pulling the main wiring harness from the top of the valve cover, he removed the primary lead from the alternator without taking off the negative battery cable. I was across the garage getting a tool when I heared *crack* as the guide touched the engine bay and the voltage spiked.

My alternator tested good, my battery tested good, here are the electrical systems that still work.

ECU
Fuel Pump
Ignition Coil

That's it.

No Windows, no Lights, no Spedometer or Tach, no A/C, no Fuel Gauge. I pulled all my fuses in the passenger compartment and they were all fine. Anyone know of a relay that could have burnt out to cause every system but the vitals to fail? Thanks for any/all of your help.

I'm picking up a Toyota service manual now. I guess I was going to need one eventually, this is just going to push the turbo setup back a ways.

-nate