It's a well known fact that silver engines are faster. S is for speed. And silver. See?
My 07 classic has a silver engine, i believe only the classics had them in 07. 06 was the last year in standards. The silver engines had the issues with second gear breaking, but at this point id say if it was gonna break it would've broke by now.
There have been a few updates over the years, but the color change was purely cosmetic. A number of bike rags called the silver engine ugly and suggested it be painted black to make it blend in more. Personally i like it to stand out as its kinda the whole point of the bike.