Duct sizing will be important in order to a) achieve proper space conditioning & b) not stress the blower motor with too much duct restriction.
I replaced the factory system because I needed/wanted the extra space it takes up and I did not want rear A/C. Sadly the Ford system is too prone to leaks in the A/C lines which is expensive to replace or repair. My air flow now is 100% through roof vents I've added to a different type ceiling cover or headliner if you will.
I measured the CFM's of the blower of the aftermarket unit and the factory unit then did as best I could replicating those figures. I ended up with two 3" diameter metal ducts, one is a 90* elbow mounted directly to the blower housing and another about 6' long terminated in another 90* elbow. Both outlets have venturi's obtained from Coyote International LLC: Coyote International Online Catalog
---this is one of the larger suppliers to the RV and van conversion outfits.
I used their Part Number 06-2012NS (non-shut off version) along with 06-2012-4 flush mounting retainer.
Since the rear unit was removed insulation was added (all rear glass covered with insulation) and an FRP commercial bathroom/kitchen sheet material applied over plywood for future attachment of various fittings etc.
BTW I completely removed all A/C components and hoses associated with the rear A/C. That was the best for the front-only A/C as it basically becomes just a front-only A/C unit, none of the pitfalls of improper capping of or blocking rear refrigerant flow in any other way.