Are 1968 and 1969 Heater/AC the same?
 

What is the difference between 1968 and 1969 GTO heater/ac box if any?

How many divertor doors are on a 1968?

I "think" the underhood components are the same with the exception of the AC compressor mount, and the 69 has a heater flow control valve in the heater hose.

They're basically the same, just slightly different. The differences are in the control panel and electrical wiring. Besides those differences, the 69 has an additional vacuum line for the coolant control valve.

So the Heater/AC box would be the same?

The MPC shows a different evaporator & case assembly part number between 68 and 69-70.
It shows the outer (engine side) assembly to be the same from 68-70

Not sure what the difference would be IRT the evaporator assembly. It might be the vacuum fittings or some other minor thing.