First off, I have checked every relay, fuse, fluid and sensor in my car.
I can't figure this out.

My top brake light (in the window) started staying on when i had the headlights turned on. The warning light in the dash for the tail lights had come on too. I could not get the thing to turn off because it is not supposed to be on all of the time. My cruise control quit working when the head lights are on.

Then it magically stopped and the warning light in the dash went out. I come back to the car an hour later, and my tail lights would not work, the side lights, turn signals and reverse lights work, but not the tail lights.

I inspected everything and found the sensor in the trunk is out, so i replaced it.
Now I am back to square one, The brake light in the window stays on, the cruise will not work if the lights are on, everything else is working properly, I have checked all of the fluids, and fuses and the sensor I bought is fine.
I want to get rid of this problem because I have a feeling whatever it is is going to kill that sensor again.
please help if you can! thanks!

Check the switch at the brake pedal. If the switch isn't depressed all the way when the brake is at rest, then your lights would stay on.

The switch at the brake pedal will stop the Cruise control from working also.

exactly where is this switch and what does it look like? I inspected the area and the mechanism for the brakes, everything is working properly and like i said the top brake light only comes on when the headlights are on, this makes me think its an electrical problem.

It sits above the brake pedal and presses against the lever the brake pedal is mounted on. The pressure on the switch is released when you press the brake pedal.

First off, I have checked every relay, fuse, fluid and sensor in my car.
I can't figure this out.

My top brake light (in the window) started staying on when i had the headlights turned on. The warning light in the dash for the tail lights had come on too.
please help if you can! thanks!
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Check the wiring harness at the trunk hinge.
Repeated flexing can cause some of the wire strands to break, changing resistance read by the tail light sensor, or interrupting current altogether.
First time I checked, one small wire inside the bundle was kinked and broke apart with gentle pulling by hand.
About a year later the problem recurred so I spliced in and soldered new wires for all of them, first coiling the new sections to increase flexibility. (wrapped around a Phillips screw driver - ended up looking like a telephone cord)

thanks more than likely you are right, there is no rely or fuse that could make the car act so wierd, its gotta be a wiring issue.