My friend and myself are fixing a 95 explorer that we are flipen so we can turn around and sell it, but we are having one problem and we dont know were to go anymore, ok so here it is

problem --- all 4 windows dont roll up or down, they worked before we had to take off the driver and pass door. we had to change window motors in drivers door.

we checked the fuses inside the car and they were all good but we still cant figure out why the windows dont work. but all the power locks work.

we got a new door and i swaped out the wiring harness from the old wrecked door into the new door from the junkyard but there is one extra connecter on the new door that we cant figure out were it goes, any help would be great if you have any info at all please let us know thanks

Your problem is circled all over the vehicle, its a ford

lol i thought about saying that too!
seriously though, you said swapped over the harness from the wrecked door into the new door so where is the new pluging at? i dont about a ford but ive had a few vehicles that also had a relay for the windowsunder the hood in the pcm you could try checking that. considering you said the old door was wrecked could there possibly be a wire that was pinched, and broke apart once it was moved around to swap the doors?