You can find most of these answers on the forums, but to save you some searching:
1. The 13 colonies are a separate faction at first. The British only start with Rupert's Land in the far north on the mainland in the beginning. It is the same for the French and Louisiana, and the Spanish and New Spain. The protectorate factions will join your empire if you complete some certain missions.
2. No. You need to mod, or complete the RTI tutorial. Then, you can play them from 1776 (?) onwards as the United States. Oh, and only the fourth stage lets you do this, because the tutorial locks the map to certain areas.
3. Only rebellions in your capital will change your government. You can choose to either fight as loyalists or reformers. There are emergent factions for nearly every territory, replacing the generic rebels. So if you screwed around with Ireland, the Irish rebel faction (Jacobites, I believe) would spring up, with their own army.
4. Random guy. I don't think you can have generals run for election, which sucks. The president is not a general, nor the monarch. They are strictly campaign map characters that can have bonuses (Or not) on certain things in your empire.
Edit: This should be obvious stuff if you followed the all the pre-release stuff.
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