So I just picked up a 69 Cougar Convertible. The previous owner told me it had some electrical issues. I managed to get it running, all new grounds, but none of the power windows work. The previous owner insists that they were working perfectly last summer. Upon investigating, it is clear that there is no power window relay, and no power window harness from the behind the dash to the missing relay. The power top is hooked up to a breaker on the starter solenoid, and the power top does work. Is there some other way that the power window relay could have been bypassed? And if so, how, as I would like to make the power windows work? I can’t find the blue wire and red wire that are supposed to go to the power window relay. Also, I’ve been told that the 69 windows will have to be changed to 70 style bolt in eventually. Although I know bolt in would be better, is there not better glue available now to fix the glue in windows without having future issues? Also, the dash is currently out of the car, but I don’t imagine that anything electrical connected to the dash would affect the power window operation. Will the power windows continually be a headache, and would you advise changing it over to manual? I have the Marti Report, and the power windows did come factory.
First welcome to the madness 
I’l assume you have some kind of schematic since your looking for blue wires, if not one of my first suggestions along with a shop manual. Can’t help you with a 69 since i’m a phat cat owner but someone will chime in. How about some pictures of the cat ? 
Not sure on the wiring, but I would keep the power windows. It sucks to have to manually roll down 4 windows every time you put the top down.
I would also keep the 69 windows. I’ve converted one to 70 windows before and didn’t like the differences.
As for a good glue to use on them, most people will tell you to use the original style channel bond, but I did that before and had to re do them a few months later. I’ve used the black eurothane glue they use for modern windshield installs on three 69’s so far and it has held up for several years with no issues. It’s not original, but who’s going to open up your door panels and look?
Go here…
http://www2.cougarpartscatalog.com/videoclips.html?attribs=87
Click on the you tube link and look up the video on 69 glue in glass… Watch that video…
I also suggest you look up their other video on the rear power pancake motor…
I have not dealt with the wiring on my XR7 power windows yet so can’t help you there… I have downloaded the wireing schematics available for free off of WCCC’s website and suggest you do the same if you do not have them…
Currently I have at least 90 percent of my interior striped out of my car so I can do the body work and re-color… I am going to re-do all of my glass glue in before re-installing it based off of WCCC videos…
Brian
where are you located? there may be some one local to give you a hand.