Need Help, electrical gremlins

I have a 1998 4.6 Mustang GT Automatic. Randomly the headlights, dash lights, dome light, power mirrors, radio, and keyless entry will stop working. I checked all the fuses and none of them were blown. Then randomly it started working again. That following night I was driving and everything stopped working again for about an hour then started working again and so on and so on. I have checked all the grounds under the hood and they are all clean. It is fuses 16, 13, 12, 8, and 4 that randomly stop getting power, I checked with a fuse light checker and those ones are not getting power when everything stops working. But when it all turns back on, they all have power again. Does anybody have any ideas as to what is happening? Help Please!!

RaggedGT said:

When all that cuts off, do you still have voltage at the alternator?

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Yes, the alternator still has voltage, I drove the car for an hour the other day when nothing was working and my voltage meter did not drop, and other electronics still work like the brake lights and turn signals.

GT4Lyfe said:

Check the small 2 or three pin plug on the alternator and ignition switch.

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I checked them, they were both clipped in still, took them out, and cleaned them with some electrical cleaner, pins all look good.