Let's see if I've got this right: I think you're saying the pad isn't touching 100% in the vertical plane, right? Not forward to back, but from top of rim sidewall to bottom? It's hard to tell in this pic of your rear brake, but I think it shows that a little riding - or sanding/filing to match the rim sidewall profile - will match it right up:
Fore/aft position looks spot-on. It's true the pad holders look to be at the limit of the caliper arms, but they still look as though they'll allow full contact with the rim sidewall once the pads match the sidewall profile.
That bike is still a beauty, Dane
DD