I have the same problem except mine isnt completely out.
Its the bearing in the motor. it is stripped. Mine goes up and down but the motor doesnt stop when the glass reaches the top or bottom and starts clicking/ popping.
Anyway I suggest you call ford and give them your Vin number and ask what the oem part number is for the window motor so that you can get one that will fit correctly. I tried an autozone replacement and it didnt fit right.
watever you dont go to the ford place, theyll charge u out the ass.
Go to Advance Auto tell them the problem(the guy came out and looked at mine), they'll order u a motor, might take a couple days to come in, they'll call you when its in, ya pick it up there and u can get a $15 back for core charge when u turn ur old motor in.
Installing mine was tricky. MAKE SURE you get someone to hold the window before you disconnect the motor IT WILL FALL. It took about an hour for me and it fit fine, works great now.