IIRC you can wangle the linkage without removing those covers. You can remove the covers though, are they not held on by 4 or so of those small and easy to lose little tin clips, right on the edges of the covers? The trouble IIRC was that I had do disconnect on one or both sides the flap control pin which was ishly hard in that tight space- and fragile/easy to damage little rods as well as the plastic flaps they drive. Those heater boxes are normally fitted (motor and all) from inside the car with the dash out- assembly is not easy with them in the car, but should be possible with the exact tools and lots of care using them, though your back may never forgive you...