First my little synopsis is indeed just that, I left out a whole bunch of plot lines and conflict that would arise in such a scenario. And since I rather not spoil my own story ideas that is going that have stay that way until I start posting.
Czechoslovakia would be Bohemia, right? Then FJ need to keep it for himself together with Austria (as Bohemia is full part of the sold Holy Roman Empire and likely still inside the German confederation)
Indeed Bohemia-Moravia(but not Slovakia), Slovenia with Trieste, Krakow, and Süd-Tirol were all part of the GC. However these areas could enter and leave the Confederation basically at the request of their Sovereign. Poznan and Prussia were entered in 1848 and withdrawn in 1851, East Luxembourg was withdrawn 1830 when it became part of Belgium, and the rest of Luxembourg and Limburg were withdrawn upon unification. Now as this is a nationalistic move areas full of non-Germans such as the Czech could, by popular demand on both sides of the demographic divide, be left out.
Recipe for disaster. The Hungarians would not accept any division of the Holy Crown lands.
Oh yes this will be one of those compromises that any true nationalist is going to hate with all their guts. However FJ has a big stick in that the Russians (for reasons that will remain unspoiled for now) are willing to intervene, and have publicly stated this.
A sizeable chunk of Prussia (East Prussia, West Prussia and Posen) also lay outside the Confederation, but no one demanded that these provinces be hived off and given to another Hohenzollern.
True but as stated these areas were full of Germans, and by most were considered to be integral parts of the German Nation. Notable objections were naturally forthcoming from the Polish living in those same areas.
However Lombard-Venice, Hungary, Croatia, and Slovakia were and are not. This is true as well for Bohemia if to a more limited extend. Especially after the limited redrawing of the borders so that the German population will be included in the new German Reich. This would have to include setting up some enclaves inside the Czech and Slovenian borders. But not inside Hungary and Slovakia as they are either to small to bother, right next to the Capital, or to far away.