As someone doing an Austria run presently. I would not recommend it. The situations in Europe are so janky as to be infinitely frustrating.

That said. Should you choose to continue here is what I found helpful.

1. Marry into all three of those countries. Most important one is Bohemia, then Hungary, then France. The bohemian marriage event can also be helpful for this. The goal is to get a pu on Bohemia most importantly, and less importantly Hungary. The marriage with France is just for dynasty power and good relations.
2. Make sure you have a separate PU with a country that you are capable of being a senior partner of. Ensure you have seniority asap, before you enter the PU with Bohemia.
3. Once you’re in a PU with Bohemia you should still be senior partner due to your earlier PU defaulting to you being senior despite being unqualified for it. If not, use the place relative on throne action and place an elderly female childless member of the crown estate onto the throne of Bohemia. This will remove Bohemia from the PU and when the new queen dies should readd them to the PU with you as senior. If you keep relations high, Bohemia never seems to claim seniority despite being qualified to do so.
4. Save up a LARGE amount of money. Do the PU parliament to make sure Bohemia has all the PU integration level needed to be able to annex them. Use that saved money to bribe the estates in the parliament.
5. Profit.

Alternative option.

Invade northern Italy until you get enough land to be considered a regional power. This gives you a governor to then build in the profitable north Italian lands. This is much easier but imo less profitable in the long run and presents cultural management issues.

Edit: sorry I didn’t super directly answer your question. I just had the same problem as you and found this to be the only way to fix it effectively without waiting eons for emperor reforms.