Habsburgs never inherit Spain

Casimir IV wasn't a king of Hungary. It definitely would be difficult, but Russia was similarly multiethnic and somehow managed to stay in power.

No, it was not. Russia has always had a dominant Russian core, just as the PLC had a dominant Polish core. That Greater PLC would not and its stability would suffer for it.
 
There would be no Sigismund Augustus, because not having to worry about Iberia, Habsburgs would not need to marry Eleanor to Manuel of Portugal, thus Max would have spare granddaughter for Sigismund the Old. And as long as there are Jagiellons around, there would not be PLC. It would be in Jagiellons' vital interest to keep their hereditary Grand Duchy of Lithuania separate from Poland.
 
If nationalism eventually hits off in this timeline, would Bohemia separate from Germany, since it is Slavic?

No way. Bohemia’s history was too strongly tied to the Holy Roman Empire for thinking seriously to a separation after the Habsburg united Germany including them

I think that it all depends on how the aftermath of the Reformation plays out. Without having to juggle Spain and likely the Low Countries the Emperor might have more time to focus on dealing with the Reformation as it begins, but I think some reckoning is inevitable and that Bohemia, because of the Hussite tradition, will more likely than not become a hotspot of the Reformation. That, in turn, may emphasize their ethnic and national identity and downplay the historical ties between the Czechs and Germans, leading to their independence from any united HRE.
 
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