Recentralize* The Holy Roman Empire was not a heavily decentralized confederacy until nearly the end of its life, the simple matter is not decentralizing it to begin with.
Oh yeah, well what do you call it's precursor
http://en.wikipedia.org/wiki/Kingdom_of_Germany and it's relationship to the other parts of the Holy Roman Empire?
Everything except Germany was a decentralized confederacy, with that guy only having as much power over non-Germany as the Holy Roman Emperor had over everything outside the personal demesne. If anything, the Hapsburgs partially centralized things, as even the post 30 years war (a low point in royal authority) was still more centralized than anything between Henry V and the Hapsburgs.
To the OP, it's not going to happen with religious disunity. The only way to make it work is the Catholic Church nips "heretics" in the bud. If non-Catholics reach 25% of the general population of the HRE or even a significant minority among its counts and margraves, the rifts will cause strife and demands for autonomy, even if no Protestant vs Catholic war like the 30 years war happen.
Actually, maybe if Henry VIII of England wasn't so eager for getting in Anne Boleyn's Pants, a Catholic league victory in the first seven years of the thirty years war might do it, if the victors convert people fast enough. Any war longer than that and the destruction and loot the mercenaries cause will delegitimize imperial authority in the eyes of the masses, and inevitably any centralization efforts would be delayed or halted by the loss of legitimacy.