Interesting ideas about patching up holes in the firewall. Although it does not appear that you have more than you should, or that someone went crazy adding holes for random accessories. I dont think that there are any that need filled...
I personally like the idea of the clean out plugs added to the sides of the cowel, but they will be very difficult to access once your fenders are back in place. You will have a fender and a hood hinge with a spring to compete with for the opening... I would personally leave the larger plugs in the front of the cowel. I clean that area out with a piece of heater hose attached to the end of my shop vac. It acts as a smaller hose and allows me to vacuum up the leaves and debris that accumulate along the sides of the under dash vent openings.
Lastly, the bolt holes in the top of inner fenders are for the front splash shields that bolt in from underneath and protect the headlight bucket and parking lights.