Hi, I was in the same situation as you some months ago...
Q1. I have one hole there instead you have 2. My searches led me to the conclusion these are additions,
not standard from the factory. I kept the hole, it is usefull for me : I am running the oil pressure sendor unit through it, and wiring of an additional ignition box fixed inside the cabin.
You can still decide differently and close/repair these holes with metal plate.
I don't use it for AC.
Q2. Yes I also did that, I am not remving the fender. I flexed my body under the car, I seated in the firewall place on the engine corssmember, and I installed a new heater delete plate. I could use my left hand to fix the plate using screws at the hidden area.
I used my old heater plate as a template for drilling fixing holes. I added a plate for hose passages.
There is fixing point on the VA box.
Here the plate check fit before painting.
Also I added on the heater delete plate inside fender, a hole for wires passages I use for electrical fan, AC compressor 12V.
Fixed in place with short screwdriver, sitting on the engine crossmember.
From the inside of the car, the kick panel vent is large enough to insert there an electric drill that you can use if needed..
Marc