Weird Electrical Problem (after tranny change)

[Cynic44642@aol.com]

Hello all,

After switching switching the automatic transmission for a manual, the power 
windows only work interminttently.  It seems that when the car has had a 
chance to sit the windows will work.  Once the car is started they cease to 
work at all.  
There are 2 wires that are still disconnected when we swapped the pedal 
assembly's, but there doesn't seem to be any terminals to hook them up to... 
the colors are red/blue and brown/grey(?).
The book isn't any help because it shows only one hot lead in and one ground 
coming out for the whole power window system...

Thanks,
Arden
85 5KS