Indeed, if you look closely you'll see that the silencers of the CB500 SITO system have much longer "ears" than the CB750 so they indeed sit lower. Hope you dont run into collector pipes diameter issues though, cant believe that the 750 and 500 have the same diameter pipes.
In any case, good luck with it
I am starting this winter to work on my Le-Mans III, so let me know if you need anything from Mandello del Lario. I go there often to get bits from Stucchi.
Cheers
TG