You need a quick victory against the French by storming Paris Castle so that you can free up some of your troops. Don't auto resolve because the French king will probably survive. When you have destroyed the French royal family, divert some of your troops to your Italian and Hungarian borders and use your emissaries to bribe the rebel provinces. Don't divert too many of your troops because sooner or later the English are going to attack you.

This stage of the campaign is always going to be hard for you since an AI faction uses the 50k starting cash to build up a large army which its provinces cannot support, so it has to invade somebody.

Even if you give economic development a high priority, the HRE simply cannot afford to adequately defend all its frontier provinces, especially since there is no way to totally eradicate the Papacy. I would pursue a military strategy of combining relatively inexpensive garrisons with 3-4 field armies, the idea being to swiftly retake land that I lose rather than prevent the loss in the first place.