why would these red and black wires be here its tapped into the window switch but runs inside cab and doesnt plug into anything ? any ideas what it could be

 

That is odd.

Here are some wild guesses.
1)Previous owner had an alarm and was trying to control the up/down ability with his keyfob
2) Previous owner thought that if he ran the power/ground wires directly to the battery, he would have the ability to roll the windows up and down with no key in the ignition
3) A function of your windows wasn't working properly and somebody was trying to run a bypass


Do all your window functions work as they should? Really, that's all that matters.

 

Are you sure they ran from the window switch? Could it be from the door lock switch possibly for an aftermarket alarm? I see in the 1st pic. They run from a harness at the door and in your second pic. Looks to be coming in from the firewall under the dash hanging there with butt connectors on the ends. Little confused with a vague description. Where are those 2 wires going under the hood in the engine room? That may help answer your question. Otherwise I'd say I agree on the wizards previous post. Possibly factory alarm or a bypass. But if everything seems to work fine without them connected I wouldn't worry much about them.