Well, if your heir is still a boy, you can get him a catholic preceptor to change his religion, and maybe his culture as well. Gregarious and diligent traits help the conversion chance IIRC, maybe zealous as well.
If you stockpile enough gold, you can create several Kingdoms (Lotharingia, Germany, maybe Italy and Burgundy), give them away and then transfer the most troublesome vassals to those new King. The huge relation ship bonus from handing out the title and vassals should be enough to make them love you, and they'll have to deal with the angry vassals themselves. Give the Kingdoms away to kinsmen, so you have the dinasty bonus but not the pretender malus. Plus it'll help your dynasty prestige.
That'll help a lot for the first years, and you'll have time to change your culture and religion before the next transition.
Be sure to keep good relations with the Pope as well, so you don't get excommunicated.
Also, if your plan calls for you to be vassal of the HRE for a while, I think there is a decision to change your culture and religion to your liege's, but it'll destroy your piety.
And if worst come to worst, you can grant independence to some of the worst vassals. Better to give away a few than having them support a pretender. You can vassalize them back once you've eased yourself into the HRE's throne anyway.