inside the engine bay on the firewall, in the middle towards the top theres this black thingiee with vent thingiees on top of it, im not sure, but isnt this the (for lack of a better term) temp regulator/flow reresistor? There is a cable attached to that, make sure its adjusted.
Accessing the flappers is a semi-pain being that you have to remove the whole dash, but with some patience, it can be done on an hour or two.
With the dash off, you should be able to tell the correct routing of the ducts. Good luck with that man, i hope you get it fixed.
Aloha!