I managed to work on the car this evening and welded up the two holes on the firewall.. They were bugging me all day! I also fixed the holes where the voltage regulator goes, since they were both oversized (explains why the voltage regulator was bolted to the inner fender) I just added weld around the holes and then ground them down and re drilled them and then ran the proper self tapping bolts into the holes. Now I won't have any future problems when it comes time to assemble.
I also drip checked a bunch of seams including the inner fender to firewall seam just to prevent water and dirt going into there.. I know it's not original, but it'll be practically unnoticeable once it dries because it sucks right into the seams and dries rock hard. I also seam sealed the A pillar area and made it close to original as possible, it's hard making it look messy after how much work I did in these areas, but that's the way it was!