mmm... dont know if it's any help, but state of the art in current supermono road racers as well as Moto 3 GP 250 singles, is two separate pipes AND two silencers.... Just a few merge the two headers into one silencer but they do it very close to it, i.e. still long separate pipes.
now that i am thinking of it, you might have seen bigger impact changing your single header "primary" lengths rather than the "secondary" collector....