I'm able to get to the pinion grub screw w/o messing with the top deck. You just have to hit it at a weird angle, and be careful you're screwing on to the flat spot when you do, otherwise you'll strip your pinion. I basically start with the pinion out on the shaft so I can reach the screw and get it on the flat spot. Then I rotate it toward the back of the car and let the wrench slide into that gap. Then I loosen the grub screw a bit to push the pinion in, get it aligned as I like it, and tighten it back down. It sounds way more complicated than it is. I too had to file the topdeck slightly so I could run larger pinions. I can't imagine it would affect anything. At least it's only a $12 part.
Are there 416 specific toe blocks yet, or will the 415 versions be what everybody uses? I'm glad to know I'm not the only one having trouble with the rear hub ballstuds coming out easily. It does seem to make a difference if you're very careful when threading them in (only thread it once) and don't overtighten.