The Pinside price seems a little high to me. Boston Pinball Ebay guide shows an average of around $400. In my opinion, old classic games in this very low price bracket don't flex much with repro parts - a nice glass, repro or original, is a simply a nice glass and that is desirable. As long as the repro is of high quality, it shouldn't have much bearing on the overall price, unless a buyer is totally opposed to repro glass.

I would price the game as a whole all things considered, and just list in ad descriptions and inform interested buyers of any repro parts on the game. If someone wants a percentage off, then you'll have to make the decision at the time if that is in your best interests.