it will with some firewall modification. if you look where the a/c unit goes you will see the 66 firewall bump out is shorter than the 69. cut out that area of the 69 firewall and weld it in the 66.
Seems to me that they are totally different systems. Is the 69 factory air or an aftermarket add-on? The compressor should work, brackets will be different. The condensor and evaporator will be different, but aren't especially expensive.. Inside the car, is where you'll find problems.